Method for producing l-beta-lysine

ABSTRACT

Purified β-amino acids are of considerable interest in the preparation of pharmacologically active compounds. Although enantiomerically pure β-amino acids, such as L-β-lysine, can be produced by standard chemical synthesis, this traditional approach is time consuming, requires expensive starting materials, and results in a racemic mixture which must be purified further. However, DNA molecules encoding lysine 2,3-aminomutase can be used to prepare L-β-lysine by methods that avoid the pitfalls of chemical synthesis. In particular, L-β-lysine can be synthesized by cultures of host cells that express recombinant lysine 2,3-aminomutase. Alternatively, such recombinant host cells can provide a source for isolating quantities of lysine 2,3-aminomutase, which in turn, can be used to produce L-β-lysine in vitro.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY-SPONSOREDRESEARCH AND DEVELOPMENT

Part of the work performed during development of this invention utilizedU.S. Government Funds, specifically NIH Grant Nos. DK28607; DK09306;GM31343; GM30480; GM10816; GM14401; GM15395; GM51806, and GM18282.Therefore, the U.S. Government has certain rights in this invention.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to DNA molecules that encode lysine2,3-aminomutase. More particularly, this invention relates to the use ofrecombinant host cells comprising such DNA molecules to produce pureL-β-lysine.

2. Related Art

Although less abundant than the corresponding α-amino acids, β-aminoacids occur in nature in both free forms and in peptides. Cardillo andTomasini, Chem. Soc. Rev. 25:77 (1996); Sewald, Amino Acids 11:397(1996). Since β-amino acids are stronger bases and weaker acids thanα-amino acid counterparts, peptides that contain a β-amino acid in placeof an α-amino acid, have a different skeleton atom pattern, resulting innew properties. For example, various peptides are protease inhibitorsbecause the presence of the β-amino-α-hydroxy acid motif acts as atransition state mimic of peptide hydrolysis.

β-Amino acids are of particular interest in the preparation ofmedicaments, such as β-lactams. Well-known β-lactam antimicrobial agentsinclude penicillins, cephalosporins, carbapenems, and monobactams. Otherexamples of medically useful molecules that contain β-amino-α-hydroxyacids include the anti-tumor agent taxol, the anti-bacterial agent,dideoxykanamicin A, bestatin, an immunological response modifier, thekynostatins, which are highly potent human immunodeficiency virus-iprotease inhibitors, and microginin, a tetrapeptide which hasanti-hypertensive properties. Accordingly, enantiomerically pureP-amino-α-hydroxy acids are of considerable importance as crucialcomponents of pharmacologically active compounds.

In the 1950′s, L-β-lysine was identified in several strongly basicpeptide antibiotics produced by Streptomyces. Antibiotics that yieldL-β-lysine upon hydrolysis include viomycin, streptolin A,streptothricin, roseothricin and geomycin. Stadtman, Adv. Enzymol.Relat. Areas Molec. Biol. 38:413 (1973). β-Lysine is also a constituentof antibiotics produced by the fungi Nocardia, such as mycomycin, andβ-lysine may be used to prepare other biologically active compounds.However, the chemical synthesis of β-lysine is time consuming, requiresexpensive starting materials, and results in a racemic mixture.

Therefore, a need exists for an improved method of preparingenantiomerically pure β-amino acids, such as β-lysine.

SUMMARY OF THE INVENTION

In one aspect, the present invention provides an isolated DNA moleculecomprising a nucleotide sequence that encodes lysine 2,3-aminomutase.

In another aspect, the present invention provides an expression vectorcomprising an isolated DNA molecule having a nucleotide sequence thatencodes lysine 2,3-aminomutase.

The present invention additionally provides a method of producing lysine2,3-aminomutase comprising the steps of culturing a host cell containingan expression vector having a nucleotide sequence that encodes lysine2,3-aminomutase and isolating lysine 2,3-aminomutase from the culturedhost cells.

The present invention provides, in a further aspect, a method ofproducing L-β-lysine from L-lysine comprising incubating L-lysine in asolution containing purified lysine 2,3-aminomutase and isolating theL-β-lysine from the solution.

Still another aspect of the present invention is a method of producingL-β-lysine from L-lysine comprising the steps of incubating culturing ahost cell in the presence of L-lysine, wherein the cultured host cellexpresses lysine 2,3-aminomutase and isolating the L-β-lysine from thecultured host cell.

DETAILED DESCRIPTION OF THE INVENTION 1. Definitions.

In the description that follows, a number of terms are utilizedextensively. Definitions are herein provided to facilitate understandingof the invention.

Structural gene. A DNA sequence that is transcribed into messenger RNA(mRNA) which is then translated into a sequence of amino acidscharacteristic of a specific polypeptide (protein).

Promoter. A DNA sequence which directs the transcription of a structuralgene to produce mRNA. Typically, a promoter is located in the 5′ regionof a gene, proximal to the start codon of a structural gene. If apromoter is an inducible promoter, then the rate of transcriptionincreases in response to an inducing agent. In contrast, the rate oftranscription is not regulated by an inducing agent if the promoter is aconstitutive promoter.

Enhancer. A promoter element. An enhancer can increase the efficiencywith which a particular gene is transcribed into mRNA irrespective ofthe distance or orientation of the enhancer relative to the start siteof transcription.

Complementary DNA (cDNA). Complementary DNA is a single-stranded DNAmolecule that is formed from an mRNA template by the enzyme reversetranscriptase. Typically, a primer complementary to portions of mRNA isemployed for the initiation of reverse transcription. Those skilled inthe art also use the term “cDNA” to refer to a double-stranded DNAmolecule derived from a single mRNA molecule.

Expression. Expression is the process by which a polypeptide is producedfrom a structural gene. The process involves transcription of the geneinto mRNA and the translation of such mRNA into polypeptide(s).

Cloning vector. A DNA molecule, such as a plasmid, cosmid, phagemid, orbacteriophage, which has the capability of replicating autonomously in ahost cell and which is used to transform cells for gene manipulation.Cloning vectors typically contain one or a small number of restrictionendonuclease recognition sites at which foreign DNA sequences may beinserted in a determinable fashion without loss of an essentialbiological function of the vector, as well as a marker gene which issuitable for use in the identification and selection of cellstransformed with the cloning vector. Marker genes typically includegenes that provide tetracycline resistance or ampicillin resistance.

Expression vector. A DNA molecule comprising a cloned structural geneencoding a foreign protein which provides the expression of the foreignprotein in a recombinant host. Typically, the expression of the clonedgene is placed under the control of (i.e., operably linked to) certainregulatory sequences such as promoter and enhancer sequences. Promotersequences may be either constitutive or inducible.

Recombinant host. A recombinant host may be any prokaryotic oreukaryotic cell which contains either a cloning vector or expressionvector. This term is also meant to include those prokaryotic oreukaryotic cells that have been genetically engineered to contain thecloned gene(s) in the chromosome or genome of the host cell.

For examples of suitable hosts, see Sambrook et al., MOLECULAR CLONING:A LABORATORY MANUAL, Second Edition, Cold Spring Harbor Laboratory, ColdSpring Harbor, New York (1989) [“Sambrook”].

As used herein, a substantially pure protein means that the desiredpurified protein is essentially free from contaminating cellularcomponents, as evidenced by a single band followingpolyacrylamide-sodium dodecyl sulfate gel electrophoresis (SDS-PAGE).The term “substantially pure” is further meant to describe a moleculewhich is homogeneous by one or more purity or homogeneitycharacteristics used by those of skill in the art. For example, asubstantially pure lysine 2,3-aminomutase will show constant andreproducible characteristics within standard experimental deviations forparameters such as the following: molecular weight, chromatographicmigration, amino acid composition, amino acid sequence, blocked orunblocked N-terminus, HPLC elution profile, biological activity, andother such parameters. The term, however, is not meant to excludeartificial or synthetic mixtures of lysine 2,3-aminomutase with othercompounds. In addition, the term is not meant to exclude lysine2,3-aminomutase fusion proteins isolated from a recombinant host.

2. Isolation of a DNA Molecule That Encodes the Clostridium Lysine2,3-Aminomutase

Lysine 2,3-aminomutase catalyzes the reversible isomerization ofL-lysine into L-β-lysine. The enzyme isolated from Clostridiumsubterminale strain SB4 is a hexameric protein of apparently identicalsubunits, which has a molecular weight of 259,000, as determined fromdiffusion and sedimentation coefficients. Chirpich et al., J. Biol.Chem. 245:1778 (1970); Aberhart et al., J. Am. Chem. Soc. 105:5461(1983); Chang et al., Biochemistry 35:11081 (1996). The clostridialenzyme contains iron-sulfur clusters, cobalt and zinc, and pyridoxal5′-phosphate, and it is activated by S-adenosylmethionine. Unliketypical adenosylcobalamin-dependent aminomutases, the clostridial enzymedoes not contain or require any species of vitamin B₁₂ coenzyme.

Although the existence of the clostridial lysine 2,3-aminomutase hasbeen known for over 25 years, there is no report in the scientificliterature on the isolation of the gene encoding the enzyme. Asdescribed herein, however, DNA molecules encoding the clostridial lysine2,3-aminomutase gene now have been isolated from a genomic library madefrom the DNA of Clostridium subterminale strain SB4. The nucleotide andpredicted amino acid sequences of clostridial lysine 2,3-aminomutase(SEQ ID NOs:1 and 2) are:

1 ATGATAAATA GAAGATATGA ATTATTTAAA GATGTTAGCG ATGCAGACTG 51 GAATGACTGGAGATGGCAAG TAAGAAACAG AATAGAAACT GTTGAAGAAC 101 TAAAGAAATA CATACCATTAACAAAAGAAG AAGAAGAAGG AGTAGCTCAA 151 TGTGTAAAAT CATTAAGAAT GGCTATTACTCCATATTATC TATCATTAAT 201 CGATCCTAAC GATCCTAATG ATCCAGTAAG AAAACAAGCTATTCCAACAG 251 CATTAGAGCT TAACAAAGCT GCTGCAGATC TTGAAGACCC ATTACATGAA301 GATACAGATT CACCAGTACC TGGATTAACT CACAGATATC CAGATAGAGT 351ATTATTATTA ATAACTGATA TGTGCTCAAT GTACTGCAGA CACTGTACAA 401 GAAGAAGATTTGCAGGACAA AGCGATGACT CTATGCCAAT GGAAAGAATA 451 GATAAAGCTA TAGATTATATCAGAAATACT CCTCAAGTTA GAGACGTATT 501 ATTATCAGGT GGAGACGCTC TTTTAGTATCTGATGAAACA TTAGAATACA 551 TCATAGCTAA ATTAAGAGAA ATACCACACG TTGAAATAGTAAGAATAGGT 601 TCAAGAACTC CAGTTGTTCT TCCACAAAGA ATAACTCCAG AACTTGTAAA651 TATGCTTAAA AAATATCATC CAGTATGGTT AAACACTCAC TTTAACCATC 701CAAATGAAAT AACAGAAGAA TCAACTAGAG CTTGTCAATT ACTTGCTGAC 751 GCAGGAGTACCTCTAGGAAA CCAATCAGTT TTATTAAGAG GAGTTAACGA 801 TTGCGTACAC GTAATGAAAGAATTAGTTAA CAAATTAGTA AAAATAAGAG 851 TAAGACCTTA CTACATCTAT CAATGTGACTTATCATTAGG ACTTGAGCAC 901 TTCAGAACTC CAGTTTCTAA AGGTATCGAA ATCATTGAAGGATTAAGAGG 951 ACATACTTCA GGATACTGCG TACCAACATT CGTTGTTGAC GCTCCAGGTG1001 GTGGTGGAAA AACACCAGTT ATGCCAAACT ACGTTATTTC ACAAAGTCAT 1051GACAAAGTAA TATTAAGAAA CTTTGAAGGT GTTATAACAA CTTATTCAGA 1101 ACCAATAAACTATACTCCAG GATGCAACTG TGATGTTTGC ACTGGCAAGA 1151 AAAAAGTTCA TAAGGTTGGAGTTGCTGGAT TATTAAACGG AGAAGGAATG 1201 GCTCTAGAAC CAGTAGGATT AGAGAGAAATAAGAGACACG TTCAAGAATA 1251 A 1 MINRRYELFK DVSDADWNDW RWQVRNRIETVEELKKYIPL TKEEEEGVAQ 51 CVKSLRMAIT PYYLSLIDPN DPNDPVRKQA IPTALELNKAAADLEDPLHE 101 DTDSPVPGLT HRYPDRVLLL ITDMCSMYCR HCTRRRFAGQ SDDSMPMERI151 DKAIDYIRNT PQVRDVLLSG GDALLVSDET LEYIIAKLRE IPHVEIVRIG 201SRTPVVLPQR ITPELVNMLK KYHPVWLNTH FNHPNEITEE STRACQLLAD 251 AGVPLGNQSVLLRGVNDCVH VMKELVNKLV KIRVRPYYIY QCDLSLGLEH 301 FRTPVSKGIE IIEGLRGHTSGYCVPTFVVD APGGGGKTPV MPNYVISQSH 351 DKVILRNFEG VITTYSEPIN YTPGCNCDVCTGKKKVHKVG VAGLLNGEGM 401 ALEPVGLERN KRHVQE

DNA molecules encoding the clostridial lysine 2,3-aminomutase gene canbe obtained by screening cDNA or genomic libraries with polynucleotideprobes having nucleotide sequences based upon SEQ ID NO:1. For example,a suitable library can be prepared by obtaining genomic DNA fromClostridium subterminale strain SB4 (ATCC No. 29748) and constructing alibrary according to standard methods. See, for example, Ausubel et al.(eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 2-1 to2-13 and 5-1 to 5-6 (John Wiley & Sons, Inc. 1995).

Alternatively, the clostridial lysine 2,3-aminomutase gene can beobtained by synthesizing DNA molecules using mutually priming longoligonucleotides. See, for example, Ausubel et al., (eds.), CURRENTPROTOCOLS IN MOLECULAR BIOLOGY, pages 8.2.8 to 8.2.13 (1990)[“Ausubel”]. Also, see Wosnick et al., Gene 60:115 (1987); and Ausubelet al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages8-8 to 8-9 (John Wiley & Sons, Inc. 1995). Established techniques usingthe polymerase chain reaction provide the ability to synthesize DNAmolecules at least 2 kilobases in length. Adang et al., Plant Molec.Biol. 21:1131 (1993); Bambot et al., PCR Methods and Applications 2:266(1993); Dillon et al., “Use of the Polymerase Chain Reaction for theRapid Construction of Synthetic Genes,” in METHODS IN MOLECULAR BIOLOGY,Vol. 15: PCR PROTOCOLS: CURRENT METHODS AND APPLICATIONS, White (ed.),pages 263-268, (Humana Press, Inc. 1993); Holowachuk et al, PCR MethodsAppl. 4:299 (1995).

Variants of clostridial lysine 2,3-aminomutase can be produced thatcontain conservative amino acid changes, compared with the parentenzyme. That is, variants can be obtained that contain one or more aminoacid substitutions of SEQ ID NO:2, in which an alkyl amino acid issubstituted for an alkyl amino acid in the clostridial lysine2,3-aminomutase amino acid sequence, an aromatic amino acid issubstituted for an aromatic amino acid in the clostridial lysine2,3-aminomutase amino acid sequence, a sulfur-containing amino acid issubstituted for a sulfur-containing amino acid in the clostridial lysine2,3-aminomutase amino acid sequence, a hydroxy-containing amino acid issubstituted for a hydroxy-containing amino acid in the clostridiallysine 2,3-aminomutase amino acid sequence, an acidic amino acid issubstituted for an acidic amino acid in the clostridial lysine2,3-aminomutase amino acid sequence, a basic amino acid is substitutedfor a basic amino acid in the clostridial lysine 2,3-aminomutase aminoacid sequence, or a dibasic monocarboxylic amino acid is substituted fora dibasic monocarboxylic amino acid in the clostridial lysine2,3-aminomutase amino acid sequence.

Among the common amino acids, for example, a “conservative amino acidsubstitution” is illustrated by a substitution among amino acids withineach of the following groups: (1) glycine, alanine, valine, leucine, andisoleucine, (2) phenylalanine, tyrosine, and tryptophan, (3) cysteineand methionine, (4) serine and threonine, (5) aspartate and glutamate,(6) glutamine and asparagine, and (7) lysine, arginine and histidine.

Conservative amino acid changes in the clostridial lysine2,3-aminomutase can be introduced by substituting nucleotides for thenucleotides recited in SEQ ID NO:1. Such “conservative amino acid”variants can be obtained, for example, by oligonucleotide-directedmutagenesis, linker-scanning mutagenesis, mutagenesis using thepolymerase chain reaction, and the like. Ausubel et al., supra, at pages8.0.3-8.5.9; Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULARBIOLOGY, 3rd Edition, pages 8-10 to 8-22 (John Wiley & Sons, Inc. 1995).Also see generally, McPherson (ed.), DIRECTED MUTAGENESIS: A PRACTICALAPPROACH, IRL Press (1991). The ability of such variants to convertL-lysine to L-β-lysine can be determined using a standard enzymeactivity assay, such as the assay described herein.

In addition, routine deletion analyses of DNA molecules can be performedto obtain “functional fragments” of the clostridial lysine2,3-aminomutase. As an illustration, DNA molecules having the nucleotidesequence of SEQ ID NO:1 can be digested with Bal31 nuclease to obtain aseries of nested deletions. The fragments are then inserted intoexpression vectors in proper reading frame, and the expressedpolypeptides are isolated and tested for lysine 2,3-aminomutase enzymeactivity. One alternative to exonuclease digestion is to useoligonucleotide-directed mutagenesis to introduce deletions or stopcodons to specify production of a desired fragment. Alternatively,particular fragments of the clostridial lysine 2,3-aminomutase gene canbe synthesized using the polymerase chain reaction. Standard techniquesfor functional analysis of proteins are described by, for example,Treuter et al., Molec. Gen. Genet. 240:113 (1993); Content et al.,“Expression and preliminary deletion analysis of the 42 kDa 2-5Asynthetase induced by human interferon,” in BIOLOGICAL INTERFERONSYSTEMS, PROCEEDINGS OF ISIR-TNO MEETING ON INTERFERON SYSTEMS, Cantell(ed.), pages 65-72 (Nijhoff 1987); Herschman, “The EGF Receptor,” inCONTROL OF ANIMAL CELL PROLIFERATION, Vol. 1, Boynton et al., (eds.)pages 169-199 (Academic Press 1985); Coumailleau et al., J. Biol. Chem.270:29270 (1995); Fukunaga et al., J. Biol. Chem. 270:25291 (1995);Yamaguchi et al., Biochem. Pharmacol. 50:1295 (1995); and Meisel et al.,Plant Molec. Biol. 30:1 (1996).

The present invention also contemplates functional fragments ofclostridial lysine 2,3-aminomutases that have conservative amino acidchanges.

3. Expression of Cloned Lysine 2,3-Aminomutase

To express the polypeptide encoded by a lysine 2,3-aminomutase gene, theDNA sequence encoding the enzyme must be operably linked to regulatorysequences that control transcriptional expression in an expressionvector and then, introduced into either a prokaryotic or eukaryotic hostcell. In addition to transcriptional regulatory sequences, such aspromoters and enhancers, expression vectors can include translationalregulatory sequences and a marker gene which is suitable for selectionof cells that carry the expression vector.

Suitable promoters for expression in a prokaryotic host can berepressible, constitutive, or inducible. Suitable promoters arewell-known to those of skill in the art and include promoters capable ofrecognizing the T4, T3, Sp6 and T7 polymerases, the P_(R) and P_(L)promoters of bacteriophage lambda, the trp, recA, heat shock, lacUV5,tac, lpp-lacλpr, phoA, gal, trc and lacZ promoters of E. coli, theα-amylase and the σ²⁸-specific promoters of B. subtilis, the promotersof the bacteriophages of Bacillus, Streptomyces promoters, the intpromoter of bacteriophage lambda, the bla promoter of the β-lactamasegene of pBR322, and the CAT promoter of the chloramphenicol acetyltransferase gene. Prokaryotic promoters are reviewed by Glick, J. Ind.Microbiol. 1:277 (1987); Watson et al., MOLECULAR BIOLOGY OF THE GENE,4th Ed., Benjamin Cummins (1987); Ausubel et al., supra, and Sambrook etal, supra.

Preferred prokaryotic hosts include E. coli, Clostridium, andHaemophilus. Suitable strains of E. coli include DH1, DH4α, DH5, DH5α,DH5αF′, DH5αMCR, DH10B, DH10B/p3, DH11S, C600, HB101, JM101, JM105,JM109, JM110, K38, RR1, Y1088, Y1089, CSH18, ER1451, BL21(DE3),BL21(DE3)plysS, BLR(DE3), BLR(DE3)plysS, and ER1647 (see, for example,Brown (Ed.), MOLECULAR BIOLOGY LABFAX, Academic Press (1991)). SuitableClostridia include Clostridium subterminale SB4 (ATCC No. 29748) andClostridium acetobutylicum (ATCC No. 824), while a suitable Haemophilushost is Haemophilus influenza (ATCC No. 33391).

An alternative host is Bacillus subtilus, including such strains asBR151, YB886, MI119, MI120, and B170. See, for example, Hardy, “BacillusCloning Methods,” in DNA CLONING: A PRACTICAL APPROACH, Glover (Ed.),IRL Press (1985).

Methods for expressing proteins in prokaryotic hosts are well-known tothose of skill in the art. See, for example, Williams et al.,“Expression of foreign proteins in E. coli using plasmid vectors andpurification of specific polyclonal antibodies,” in DNA CLONING 2:EXPRESSION SYSTEMS, 2nd Edition, Glover et al. (eds.), pages 15-58(Oxford University Press 1995). Also see, Ward et al., “GeneticManipulation and Expression of Antibodies,” in MONOCLONAL ANTIBODIES:PRINCIPLES AND APPLICATIONS, pages 137-185 (Wiley-Liss, Inc. 1995); andGeorgiou, “Expression of Proteins in Bacteria,” in PROTEIN ENGINEERING:PRINCIPLES AND PRACTICE, Cleland et al. (eds.), pages 101-127 (JohnWiley & Sons, Inc. 1996).

An expression vector can be introduced into bacterial host cells using avariety of techniques including calcium chloride transformation,electroporation, and the like. See, for example, Ausubel et al. (eds.),SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 1-1 to 1-24(John Wiley & Sons, Inc. 1995).

To maximize recovery of functional lysine 2,3-aminomutase fromrecombinant hosts, transformed cells should be cultured under anaerobicconditions. Methods for culturing recombinant clostridia are well-knownto those of skill in the art. See, for example, Mermelstein et al., Ann.N.Y. Acad. Sci. 721:54 (1994); Walter et al., Ann. N.Y. Acad. Sci.721:69. (1994). Additionally, anaerobic culturing of bacteria is wellknown in the art. See, for example, Smith and Neidhardt, J. Bacteriol.154:336 (1983).

4. Isolation of Cloned Lysine 2,3-Aminomutase and Production ofAnti-Lysine 2,3-Aminomutase Antibodies

(a) Isolation of Recombinant Lysine 2,3-Aminomutase

General methods for recovering protein produced by a bacterial systemare provided by, for example, Grisshammer et al., “Purification ofover-produced proteins from E. coli cells,” in DNA CLONING 2: EXPRESSIONSYSTEMS, 2nd Edition, Glover et al. (eds.), pages 59-92 (OxfordUniversity Press 1995); Georgiou, “Expression of Proteins in Bacteria,”in PROTEIN ENGINEERING: PRINCIPLES AND PRACTICE, Cleland et al. (eds.),pages 101-127 (Wiley-Liss, Inc. 1996).

Recombinant lysine 2,3-aminomutases can be purified from bacteria usingstandard methods that have been used to purify Clostridium subterminaleSB4 lysine 2,3-aminomutase. In general, several precautions can be takento ensure high enzyme activity of the purified protein. As discussedabove, for example, enzyme activity will be maximal when host cells arecultured under anaerobic conditions. Frey and Reed, Adv. Enzymol. 66:1(1993). Oxygen should also be excluded during all purification steps.Purification under anaerobic conditions protects metal cofactors frombeing irreversibly degraded and allows maximal activity to be attainedupon activation with S-adenosylmethionine.

Enzyme activity of isolated lysine 2,3-aminomutase can also be maximizedby including cobalt in culture media and purification buffers. Suitableculture media, for example, contain 10-100 μM CoCl₂, while purificationbuffers may contain 5 μM CoCl₂. Culture media may also contain 10-100 μMFe²⁺. In addition, the inclusion of pyridoxal 5′-phosphate and lysine inpurification buffers will aid in the stabilization of enzyme activity.For example, purification buffers may contain 10-100 μM pyridoxal5′-phosphate and 100 μM lysine.

As an illustration, recombinant bacterial host cells that over-producelysine 2,3-aminomutase can be cultured under anaerobic conditions inmedium described by Chirpich et al., J. Biol. Chem. 245:1778 (1970),which also contains 100 μM ferric ammonium sulfate and 100 μM cobaltchloride. Typically, cells are harvested at A₆₆₀ values of 0.5 to 0.7.

The enzyme can be purified according to the procedure of Moss and Frey,J. Biol. Chem. 265:18112 (1990), as modified by Petrovich et al., J.Biol. Chem. 226:7656 (1991). In this procedure, all steps are performedin standard buffer, which consists of 30 mM Tris-HCl (pH 8.0), 0.1 mMdithiothreitol, 0.1 mM pyridoxal phosphate, 0.1 mM lysine, and 4.0 ml ofa saturated solution of phenylmethanesulfonylflouride (in 95% ethanol)per liter of buffer. All steps are carried out at 0-4° C.Centrifugations can be performed in a Sorvall RC-5 centrifuge with a GSArotor. Sonication and streptomycin sulfate precipitation steps areperformed in a glove box under nitrogen. During all other steps, astream of nitrogen or argon is maintained over the protein at all times,and all containers are flushed with argon before use. Alternatively, allsteps, from cell disruption through chromatographic separations, can beperformed in a nitrogen atmosphere in a Coy anaerobic chamber.

According to this method, fifty grams of bacterial cells are thawed andwashed in 100 ml of standard buffer. The washed pellet is resuspended in65 ml of standard buffer and sonicated using a Sonifier (Ultrasonics,Model W255R) at 72% of maximum power for a total of four minutes in oneminute bursts. The solution should be cooled to 4° C. between bursts.After adding an additional 10 ml of buffer, the solution is centrifugedat 13,000 rpm for 30 minutes.

The supernatant fluid, including the viscous layer above the pellet, isdecanted, and 25 ml of a 14% solution of streptomycin sulfate instandard buffer is added dropwise over a period of 30 minutes. Thesuspension is then centrifuged at 13,000 rpm for 45 minutes.

After measuring the volume of supernatant fluid, sufficient solidammonium sulfate is added during 10 minutes to give a solution 42%saturated in ammonium sulfate, which is then stirred for an additional40 minutes. The suspension is centrifuged for 30 minutes at 13,000 rpm,the pellet is discarded, the volume of the liquid layer is measured, andsufficient ammonium sulfate is added to give a solution 52% saturated inammonium sulfate. After centrifugation at 13,000 rpm for 45 minutes, theresulting pellet is resuspended in 4-5 ml of standard buffer (finalvolume: 12-15 ml).

The isolated protein is then applied to a 100 ml column of PhenylSepharose equilibrated with standard buffer that also contains 2 Mammonium sulfate. The column is eluted with a linear gradient,decreasing from 2 M to 0 M ammonium sulfate in the same buffer, using atotal volume of one liter, at a flow rate of 1.5-2 ml per minute. Tenmilliliter fractions are collected. The column is then washed with anadditional 250 ml of the same buffer less ammonium sulfate. Thefractions containing lysine 2,3-aminomutase are located by A₄₁₀measurements and activity assays. The enzyme typically elutes from thecolumn just before the end of the gradient. Active fractions arecombined and the protein is concentrated by the addition of ammoniumsulfate to 75% saturation, followed by stirring for 45 minutes. Aftercentrifugation at 9,000 rpm for 40 minutes, the pellet is frozen withliquid nitrogen and stored at −70° C.

The enzyme can be purified further by ion exchange chromatographythrough a 50-ml column of QAE Sepharose, followed by gel permeationthrough a column (2.7×37 cm, 210 ml) of Sephacryl S-300 superfine.Petrovich et al., J. Biol. Chem. 226:7656 (1991).

The above procedure can be used to obtain enzyme preparations that aretypically homogenous and that migrate as a single prominent band(M_(r)=47,000). Isolated lysine 2,3-aminomutase appears to be about 90%pure, although a very few faint additional bands may appear on heavilyloaded SDS-PAGE gels.

Additional variations in purification are described by Petrovich et al.,J. Biol. Chem. 226:7656 (1991), and can be devised by those of skill inthe art. For example, anti-lysine 2,3-aminomutase antibodies, obtainedas described below, can be used to isolate large quantities of lysine2,3-aminomutase by immunoaffinity purification.

Lysine 2,3-aminomutase activity can be determined by measuring theconversion of radiolabeled L-lysine to radiolabeled L-β-lysine. Forexample, Chirpich et al., J. Biol. Chem. 245:1778 (1970), describe aradioenzyme assay using ¹⁴C-labeled L-lysine. Briefly, an enzymeactivation solution is prepared by mixing the following components inthe following order: sufficient distilled water to give a final volumeof 120 μl, 5.0 μl of 1.0 M Tris-HCl (pH 8.2), 5.0 μl of 1.2 mM pyridoxalphosphate, test enzyme, 5.0 μl of 0.3 M glutathione (pH 8.3), 5.0 μl of24 mM ferrous ammonium sulfate, and 5.0 μl of 24 mM sodium dithionite.During mixing, a flow of argon should be maintained to the bottom oftubes to protect auto-oxidizable components.

Immediately after addition of dithionite, tubes are mixed gently toavoid exposure of the solution to air. An acid-washed glass capillary(14 cm long×0.8 mm inner diameter) is filled with the activationsolution until about one centimeter of free space remains at each end.After sealing both ends with a gas-oxygen torch, capillary tubes areincubated in a 37° C. water bath for 60 minutes. After incubation,capillary tubes are broken at one end, and a 5 μl aliquot of activatedenzyme solution is removed from the center using a 10 μl Hamiltonsyringe and assayed.

Components for the assay solution are added to tubes in the followingorder: 35 μl of distilled water, 5 μl of 0.3 M Tris-HCl (pH 7.8), 5.0 μlof 0.12 M ¹⁴C-labeled L-lysine (0.033 μCi per μmole, uniformly labeled),5.0 μl of 46 μM S-adenosylmethionine (in 10 mM HCl), 5 μl of 12 mMsodium dithionite, and 5 μl of activated enzyme. Just before addition ofdithionite, a flow of argon is started to avoid oxidation. Each sampleis sealed in a capillary tube and incubated for 15 minutes in a 30° C.water bath. The reaction is stopped by adding the reaction mixture to 30μl of 0.4 N formic acid.

Lysine and β-lysine in the acidified reaction mixture are separated bypaper ionophoresis. For each determination, 5 μl of carrier β-lysine (10mM) and two 5 μl aliquots of the acidified reaction mixture are appliedalong a line near the middle of a sheet of filter paper (56×46 cm).After ionophoresis, the amino acids are located by dipping the driedpaper in 0.01% ninhydrin in acetone. The spots are cut out and countedin a scintillation counter.

The basic assay protocol of Chirpich et al. can be varied. For example,the activation solution can be modified by replacing glutathione withdihydrolipoate, and ferrous ammonium sulfate can be replaced with fenicammonium sulfate. Moss and Perry, J. Biol. Chem. 262:14859 (1987). Inanother variation, the test enzyme can be activated by incubation at 30°C. for six hours. Petrovich et al., J. Biol. Chem. 266:7656 (1991).Moreover, Ballinger et al., Biochemistry 31:949 (1992), describe severalmodifications of the basic method including the use of an anaerobicchamber to perform the entire procedure. Those of skill in the art candevise further modifications of the assay protocol.

(b) Preparation of Anti-Lysine 2,3-Aminomutase Antibodies and FragmentsThereof

Antibodies to lysine 2,3-aminomutase can be obtained, for example, usingthe product of an expression vector as an antigen. Polyclonal antibodiesto recombinant enzyme can be prepared using methods well-known to thoseof skill in the art. See, for example, Green et al., “Production ofPolyclonal Antisera,” in IMMUNOCHEMICAL PROTOCOLS (Manson, ed.), pages1-5 (Humana Press 1992). Also see, Williams et al., “Expression offoreign proteins in E. coli using plasmid vectors and purification ofspecific polyclonal antibodies,” in DNA CLONING 2: EXPRESSION SYSTEMS,2nd Edition, Glover et al. (eds.), pages 15-58 (Oxford University Press1995).

Alternatively, an anti-lysine 2,3-aminomutase antibody can be derivedfrom a rodent monoclonal antibody (MAb). Rodent monoclonal antibodies tospecific antigens may be obtained by methods known to those skilled inthe art. See, for example, Kohler et al, Nature 256:495 (1975), andColigan et al (eds.), CURRENT PROTOCOLS IN IMMUNOLOGY, VOL. 1, pages2.5.1-2.6.7 (John Wiley & Sons 1991) [“Coligan”]. Also see, Picksley etal, “Production of monoclonal antibodies against proteins expressed inE. coli,” in DNA CLONING 2: EXPRESSION SYSTEMS, 2nd Edition, Glover etal (eds.), pages 93-122 (Oxford University Press 1995).

Briefly, monoclonal antibodies can be obtained by injecting mice with acomposition comprising an antigen, verifying the presence of antibodyproduction by removing a serum sample, removing the spleen to obtainB-lymphocytes, fusing the B-lymphocytes with myeloma cells to producehybridomas, cloning the hybridomas, selecting positive clones whichproduce antibodies to the antigen, culturing the clones that produceantibodies to the antigen, and isolating the antibodies from thehybridoma cultures.

MAbs can be isolated and purified from hybridoma cultures by a varietyof well-established techniques. Such isolation techniques includeaffinity chromatography with Protein-A Sepharose, size-exclusionchromatography, and ion-exchange chromatography. See, for example,Coligan at pages 2.7.1-2.7.12 and pages 2.9.1-2.9.3. Also, see Baines etal., “Purification of Inmunoglobulin G (IgG),” in METHODS IN MOLECULARBIOLOGY, VOL. 10, pages 79-104 (The Humana Press, Inc. 1992).

For particular uses, it may be desirable to prepare fragments ofanti-lysine 2,3-aminomutase antibodies. Such antibody fragments can beobtained, for example, by proteolytic hydrolysis of the antibody.Antibody fragments can be obtained by pepsin or papain digestion ofwhole antibodies by conventional methods. As an illustration, antibodyfragments can be produced by enzymatic cleavage of antibodies withpepsin to provide a 5S fragment denoted F(ab′)₂. This fragment can befurther cleaved using a thiol reducing agent to produce 3.5S Fab′monovalent fragments. Optionally, the cleavage reaction can be performedusing a blocking group for the sulfhydryl groups that result fromcleavage of disulfide linkages. As an alternative, an enzymatic cleavageusing pepsin produces two monovalent Fab fragments and an Fc fragmentdirectly. These methods are described, for example, by Goldenberg, U.S.Pat. Nos. 4,036,945 and 4,331,647 and references contained therein.Also, see Nisonoffet al., Arch Biochem. Biophys. 89:230 (1960); Porter,Biochem. J. 73:119 (1959), Edelman et al., in METHODS IN ENZYMOLOGY VOL.1, page 422 (Academic Press 1967), and Coligan at pages 2.8.1-2.8.10 and2.10.-2.10.4.

Other methods of cleaving antibodies, such as separation of heavy chainsto form monovalent light-heavy chain fragments, further cleavage offragments, or other enzymatic, chemical or genetic techniques may alsobe used, so long as the fragments bind to the antigen that is recognizedby the intact antibody.

For example, Fv fragments comprise an association of V_(H) and V_(L)chains. This association can be noncovalent, as described in Inbar etal., Proc. Nat'l Acad. Sci. USA 69:2659 (1972). Alternatively, thevariable chains can be linked by an intermolecular disulfide bond orcross-linked by chemicals such as glutaraldehyde. See, for example,Sandhu, Crit. Rev. Biotech. 12:437 (1992).

Preferably, the Fv fragments comprise V_(H) and V_(L) chains which areconnected by a peptide linker. These single-chain antigen bindingproteins (sFv) are prepared by constructing a structural gene comprisingDNA sequences encoding the V_(H) and V_(L) domains which are connectedby an oligonucleotide. The structural gene is inserted into anexpression vector which is subsequently introduced into a host cell,such as E. coli. The recombinant host cells synthesize a singlepolypeptide chain with a linker peptide bridging the two V domains.Methods for producing sFvs are described, for example, by Whitlow etal., Methods: A Companion to Methods in Enzymology 2:97 (1991). Also seeBird et al., Science 242:423 (1988), Ladner et al., U.S. Pat. No.4,946,778, Pack et al., Bio/Technology 11:1271 (1993), and Sandhu,supra.

Another form of an antibody fragment is a peptide coding for a singlecomplementarity-determining region (CDR). CDR peptides (“minimalrecognition units”) can be obtained by constructing genes encoding theCDR of an antibody of interest. Such genes are prepared, for example, byusing the polymerase chain reaction to synthesize the variable regionfrom RNA of antibody-producing cells. See, for example, Larrick et al.,Methods: A Companion to Methods in Enzymology 2:106 (1991);Courtenay-Luck, “Genetic Manipulation of Monoclonal Antibodies,” inMONOCLONAL ANTIBODIES: PRODUCTION, ENGINEERING AND CLINICAL APPLICATION,Ritter et al. (eds.), pages 166-179 (Cambridge University Press 1995);and Ward et al., “Genetic Manipulation and Expression of Antibodies,” inMONOCLONAL ANTIBODIES: PRINCIPLES AND APPLICATIONS, Birch et al.,(eds.), pages 137-185 (Wiley-Liss, Inc. 1995).

5. Isolation of Additional Lysine 2,3-Aminomutase Genes

The nucleotide sequences of the clostridial lysine 2,3-aminomutase geneand antibodies to the enzyme provide a means to isolate additionallysine 2,3-aminomutase genes. Such genes can encode enzymes from variousorganisms, including Porphyromonas, Bacillus, Deinococcus, Aquifex,Treponema, Haemophilus, Escherichia, and Streptomyces.

For example, the amino acid sequence of the clostridial lysine2,3-aminomutase was used to identify related enzymes in variousbacteria. Sequence analyses revealed a sequence identity of about 72%,64%, 54%, 48%, 39%, 33% and 31% between the amino acid sequence of theclostridial enzyme and unknown gene products of Porphyromonas gingivalis(incomplete genome, The Institute for Genomic Research “TIGR”hypothetical protein), Bacillus subtilus (AF015775), Deinococcusradiodurans (incomplete genome, TIGR hypothetical protein), Aquifexaeolicus (AE000690), Treponema pallidum (AEOO1197), Haemophilusinfluenza (P44641), and Escherichia coli (P39280) respectively. Thenucleotide and amino acid sequences (SEQ ID NOs:3 and 4) of the E. colipolypeptide are:

1 ATGGCGCATATTGTAACCCTAAATACCCCATCCAGAGAAGATTGGTTAACGCAACTTGCC 61GATGTTGTGACCGATCCTGATGAACTTCTGCGTCTTTTGAATATAGACGCGGAGGAAAAA 121CTGTTAGCCGGACGCAGCGCCAAAAAGCTTTTTGCCCTGCGTGTGCCCCGCTCATTTATC 181GATCGCATGGAGAAAGGCAATCCGGACGATCCTCTTTTGCGTCAGGTACTTACCTCGCAA 241GATGAGTTTGTCATCGCGCCCGGATTCTCCACCGACCCACTGGAAGAACAGCACAGCGTA 301GTGCCTGGTTTGTTGCATAAATACCACAACCGGGCGCTTTTGCTGGTCAAAGGCGGCTGC 361GCGGTAAATTGCCGCTATTGCTTCCGTCGTCACTTCCCCTATGCCGAAAATCAGGGCAAC 421AAGCGTAACTGGCAAACTGCACTTGAGTATGTTGCTGCGCATCCGGAACTGGACGAGATG 481ATTTTCTCCGGCGGCGATCCGCTGATGGCGAAAGATCACGAGCTGGACTGGTTGCTCACA 541CAACTGGAAGCCATCCCGCATATAAAACGTCTGCGGATTCACAGCCGTCTGCCGATTGTG 601ATCCCGGCACGTATCACCGAGGCGCTGGTTGAATGCTTTGCCCGTTCTACGCTGCAAATC 661TTGCTGGTGAATCACATCAACCATGCCAATGAGGTAGATGAAACATTCCGTCAGGCGATG 721GCTAAGTTGCGCCGGGTAGGCGTTACTTTGCTGAACCAGAGCGTTCTGTTACGTGATGTG 781AACGATAACGCACAAACGCTGGCAAACCTGAGTAATGCGTTGTTCGATGCCGGCGTAATG 841CCGTATTACCTGCATGTGCTCGATAAAGTACAGGGCGCGGCGCATTTTATGGTGAGTGAT 901GACGAAGCACGGCAGATTATGCGTGAGTTGCTGACACTGGTGTCGGGATATCTGGTGCCG 961AAACTGGCGCGAGAAATTGGCGGCGAACCCAGCAAAACGCCGCTGGATCTCCAGCTACGC 1021CAGCAGTAA 1 MAHIVTLNTPSREDWLTQLADVVTDPDELLRLLNIDAEEKLLAGRSAKKL 51FALRVPRSFIDRMEKGNPDDPLLRQVLTSQDEFVIAPGFSTDPLEEQHSV 101VPGLLHKYHNRALLLVKGGCAVNCRYCFRRHFPYAENQGNKRNWQTALEY 151VAAHPELDEMIFSGGDPLMAKDHELDWLLTQLEAIPHIKRLRIHSRLPIV 201IPARITEALVECFARSTLQILLVNHINHANEVDETFRQAMAKLRRVGVTL 251LNQSVLLRDVNDNAQTLANLSNALFDAGVMPYYLHVLDKVQGAAHFMVSD 301DEARQIMRELLTLVSGYLVPKLAREIGGEPSKTPLDLQLRQQ

The nucleotide and amino acid sequences (SEQ ID NOs: 5 and 6) of the H.influenza polypeptide are:

1 ATGCGTATTTTACCCCAAGAACCCGTCATTAGAGAAGAACAAAATTGGCTCACAATTCTA 61AAAAATGCCATTTCAGATCCTAAATTATTACTAAAAGCCTTAAATTTACCAGAAGATGAT 121TTTGAGCAATCCATTGCTGCGCGGAAACTTTTTTCGCTCCGCGTGCCACAACCTTTCATT 181GATAAAATAGAAAAAGGTAATCCGCAAGATCCCCTTTTCTTGCAAGTGATGTGTTCTGAT 241TTAGAGTTTGTGCAAGCGGAGGGATTTAGTACGGATCCCTTAGAAGAAAAAAATGCCAAT 301GCGGTGCCAAATATTCTTCATAAATATAGAAATCGCTTGCTCTTTATGGCAAAAGGCGGT 361TGTGCGGTGAATTGTCGTTATTGCTTTCGCCGACATTTTCCTTACGATGAAAACCCAGGA 421AATAAAAAAAGCTGGCAACTGGCGTTAGATTACATTGCGGCACATTCTGAAATAGAAGAA 481GTGATTTTTTCAGGTGGCGATCCTTTAATGGCGAAAGATCACGAATTAGCGTGGTTAATA 541AAACATTTGGAAAATATACCGCACTTACAACGTTTGCGTATTCACACCCGTTTGCCTGTT 601GTGATTCCGCAACGGATTACTGATGAATTTTGCACTTTATTAGCAGAAACTCGTTTGCAA 661ACAGTTATGGTGACACACATTAATCACCCGAATGAAATTGATCAAATTTTTGCTCATGCG 721ATGCAAAAATTAAACGCCGTGAATGTCACGCTTTTGAATCAATCTGTTTTGCTAAAAGGC 781GTGAATGATGATGCGCAAATTCTAAAAATATTGAGCGATAAACTTTTTCAAACAGGCATT 841TTGCCTTATTACTTGCATTTGCTGGATAAAGTTCAAGGGGCGAGCCATTTTTTGATTAGC 901GATATTGAAGCTATGCAAATCTATAAAACCTTGCAATCTCTGACTTCTGGCTATCTTGTT 961CCTAAACTTGCACGAGAAATTGCGGGCGAGCCAAATAAGACTTTATACGCAGAATAA 1MRILPQEPVIREEQNWLTILKNAISDPKLLLKALNLPEDDFEQSIAARKL 51FSLRVPQPFIDKIEKGNPQDPLFLQVMCSDLEFVQAEGFSTDPLEEKNAN 101AVPNILHKYRNRLLFMAKGGCAVNCRYCFRRHFPYDENPGNKKSWQLALD 151YIAAHSEIEEVIFSGGDPLMAKDHELAWLIKHLENIPHLQRIRIHTRLPV 201VIPQRITDEFCTLLAETRLQTVMVTHINHPNEIDQIFAHAMQKLNAVNVT 251LLNQSVLLKGVNDDAQILKILSDKLFQTGILPYYLHLLDKVQGASHFLIS 301DIEAMQIYKTLQSLTSGYLVPKLAREIAGEPNKTLYAE

The nucleotide and amino acid sequences (SEQ ID NOs: 7 and 8) of the P.gingivalis polypeptide are:

1 ATGGCAGAAA GTCGTAGAAA GTATTATTTC CCTGATGTCA CCGATGAGCA 51 ATGGAACGACTGGCATTGGC AGGTCCTCAA TCGAATTGAG ACGCTCGACC 101 AGCTGAAAAA GTACGTTACACTCACCGCTG AAGAAGAAGA GGGAGTAAAA 151 GAATCGCTCA AAGTACTCCG AATGGCTATCACACCTTATT ATTTGAGTTT 201 GATAGACCCC GAGAATCCTA ATTGTCCGAT TCGTAAACAAGCCATTCCTA 251 CTCATCAGGA ACTGGTACGT GCTCCTGAAG ATCAGGTAGA CCCACTTAGT301 GAAGATGAAG ATTCGCCCGT ACCCGGACTG ACTCATCGTT ATCCGGATCG 351TGTATTGTTC CTTATCACGG ACAAATGTTC GATGTACTGT CGTCATTGTA 401 CTCGCCGTCGCTTCGCAGGA CAGAAAGATG CTTCTTCTCC TTCTGAGCGC 451 ATCGATCGAT GCATTGACTATATAGCCAAT ACACCGACAG TCCGCGATGT 501 TTTGCTATCG GGAGGCGATG CCCTCCTTGTCAGCGACGAA CGCTTGGAAT 551 ACATATTGAA GCGTCTGCGC GAAATACCTC ATGTGGAGATTGTTCGTATA 601 GGAAGCCGTA CGCCGGTAGT CCTTCCTCAG CGTATAACGC CTCAATTGGT651 GGATATGCTC AAAAAATATC ATCCGGTGTG GCTGAACACT CACTTCAACC 701ACCCGAATGA AGTTACCGAA GAAGCAGTAG AGGCTTGTGA AAGAATGGCC 751 AATGCCGGTATTCCGTTGGG TAACCAAACG GTTTTATTGC GTGGAATCAA 801 TGATTGTACA CATGTGATGAAGAGATTGGT ACATTTGCTG GTAAAGATGC 851 GTGTGCGTCC TTACTATATA TATGTATGCGATCTTTCGCT TGGAATAGGT 901 CATTTCCGCA CGCCGGTATC TAAAGGAATC GAAATTATCGAAAATTTGCG 951 CGGACACACC TCGGGCTATG CTGTTCCTAC CTTTGTGGTA GATGCTCCGG1001 GGGGTGGTGG TAAGATACCT GTAATGCCGA ACTATGTTGT ATCTCAGTCC 1051CCACGACATG TGGTTCTTCG CAATTATGAA GGTGTTATCA CAACCTATAC 1101 GGAGCCGGAGAATTATCATG AGGAGTGTGA TTGTGAGGAC TGTCGAGCCG 1151 GTAAGCATAA AGAGGGTGTAGCTGCACTTT CCGGAGGTCA GCAGTTGGCT 1201 ATCGAGCCTT CCGACTTAGC TCGCAAAAAACGCAAGTTTG ATAAGAACTG 1251 A 1 MAESRRKYYF PDVTDEQWND WHWQVLNRIETLDQLKKYVT LTAEEEEGVK 51 ESLKVLRMAI TPYYLSLIDP ENPNCPIRKQ AIPTHQELVRAPEDQVDPLS 101 EDEDSPVPGL THRYPDRVLF LITDKCSMYC RHCTRRRFAG QKDASSPSER151 IDRCIDYIAN TPTVRDVLLS GGDALLVSDE RLEYILKRLR EIPHVEIVRI 201GSRTPVVLPQ RITPQLVDML KKYHPVWLNT HFNHPNEVTE EAVEACERMA 251 NAGIPLGNQTVLLRGINDCT HVMKRLVHLL VKMRVRPYYI YVCDLSLGIG 301 HFRTPVSKGI EIIENLRGHTSGYAVPTFVV DAPGGGGKIP VMPNYVVSQS 351 PRHVVLRNYE GVITTYTEPE NYHEECDCEDCRAGKHKEGV AALSGGQQLA 401 IEPSDLARKK RKFDKN

The nucleotide and amino acid sequences (SEQ ID NOs: 9 and 10) of the B.subtilus polypeptide are:

1 TTGAAAAACA AATGGTATAA ACCGAAACGG CATTGGAAGG AGATCGAGTT 51 ATGGAAGGACGTTCCGGAAG AGAAATGGAA CGATTGGCTT TGGCAGCTGA 101 CACACACTGT AAGAACGTTAGATGATTTAA AGAAAGTCAT TAATCTGACC 151 GAGGATGAAG AGGAAGGCGT CAGAATTTCTACCAAAACGA TCCCCTTAAA 201 TATTACACCT TACTATGCTT CTTTAATGGA CCCCGACAATCCGAGATGCC 251 CGGTACGCAT GCAGTCTGTG CCGCTTTCTG AAGAAATGCA CAAAACAAAA301 TACGATCTGG AAGACCCGCT TCATGAGGAT GAAGATTCAC CGGTACCCGG 351TCTGACACAC CGCTATCCCG ACCGTGTGCT GTTTCTTGTC ACGAATCAAT 401 GTTCCATGTACTGCCGCTAC TGCACAAGAA GGCGCTTTTC CGGACAAATC 451 GGAATGGGCG TCCCCAAAAAACAGCTTGAT GCTGCAATTG CTTATATCCG 501 GGAAACACCC GAAATCCGCG ATTGTTTAATTTCAGGCGGT GATGGGCTGC 551 TCATCAACGA CCAAATTTTA GAATATATTT TAAAAGAGCTGCGCAGCATT 601 CCGCATCTGG AAGTCATCAG AATCGGAACA AGAGCTCCCG TCGTCTTTCC651 GCAGCGCATT ACCGATCATC TGTGCGAGAT ATTGAAAAAA TATCATCCGG 701TCTGGCTGAA CACCCATTTT AACACAAGCA TCGAAATGAC AGAAGAATCC 751 GTTGAGGCATGTGAAAAGCT GGTGAACGCG GGAGTGCCGG TCGGAAATCA 801 GGCTGTCGTA TTAGCAGGTATTAATGATTC GGTTCCAATT ATGAAAAAGC 851 TCATGCATGA CTTGGTAAAA ATCAGAGTCCGTCCTTATTA TATTTACCAA 901 TGTGATCTGT CAGAAGGAAT AGGGCATTTC AGAGCTCCTGTTTCCAAAGG 951 TTTGGAGATC ATTGAAGGGC TGAGAGGTCA TACCTCAGGC TATGCGGTTC1001 CTACCTTTGT CGTTGACGCA CCAGGCGGAG GAGGTAAAAT CGCCCTGCAG 1051CCAAACTATG TCCTGTCACA AAGTCCTGAC AAAGTGATCT TAAGAAATTT 1101 TGAAGGTGTGATTACGTCAT ATCCGGAACC AGAGAATTAT ATCCCCAATC 1151 AGGCAGACGC CTATTTTGAGTCCGTTTTCC CTGAAACCGC TGACAAAAAG 1201 GAGCCGATCG GGCTGAGTGC CATTTTTGCTGACAAAGAAG TTTCGTTTAC 1251 ACCTGAAAAT GTAGACAGAA TCAAAAGGAG AGAGGCATACATCGCAAATC 1301 CGGAGCATGA AACATTAAAA GATCGGCGTG AGAAAAGAGA TCAGCTCAAA1351 GAAAAGAAAT TTTTGGCGCA GCAGAAAAAA CAGAAAGAGA CTGAATGCGG 1401AGGGGATTCT TCATGA 1 LKNKWYKYKR HWKEIELWKD VPEEKWNDWL WQLTHTVRTLDDLKKVINLT 51 EDEEEGVRIS TKTIPLNITP YYASLMDPDN PRCPVRMQSV PLSEEMHKTK 101YDLEDPLHED EDSPVPGLTH RYPDRVLFLV TNQCSMYCRY CTRRRFSGQI 151 GMGVPKKQLDAAIAYIRETP EIRDCLISGG DGLLINDQIL EYILKELRSI 201 PHLEVIRIGT RAPVVFPQRITDHLCEILKK YHPVWLNTHF NTSLEMTEES 251 VEACEKLVNA GVPVGNQAVV LAGINDSVPIMKKLMHDLVK IRVRPYYIYQ 301 CDLSEGIGHF RAPVSKGLEI IEGLRGHTSG YAVPTFVVDAPGGGGKIALQ 351 PNYVLSQSPD KVILRNFEGV ITSYPEPENY IPNQADAYFE SVFPETADKK401 EPIGLSAIFA DKEVSFTPEN VDRIKRREAY IANPEHETLK DRREKRDQLK 451EKKFLAQQKK QKETECGGDS S

nucleotide and amino acid sequences (SEQ ID NOs: 11 and 12) of the D.radiodurans polypeptide are:

1 TGGCAAGGCG TACCCGACGA GCAGTGGTAC GACTGGAAAT GGCAGCTCAA 51 GAACCGCATCAACAGTGTGG AGGAGTTGCA GGAAGTCCTG ACCCTCACCG 101 AGTCCGAGTA CCGGGGTGCGTCCGCCGAGG GCATTTTCCG CCTCGACATC 151 ACGCCGTATT TCGCGTCCCT CATGGACCCCGAAGACCCCA CCTGCCCGGT 201 GCGCCGTCAG GTGATTCCCA CCGAGGAGGA GCTCCAGCCGTTCACCTCCA 251 TGATGGAAGA CTCTCTCGCG GAGGATAAGC ACTCGCCCGT GCCGGGGCTG301 GTGCACCGCT ACCCCGACCG CGTGCTGATG CTGGTCACGA CCCAGTGCGC 351GAGCTACTGC CGCTACTGCA CCCGAAGCCG CATCGTGGGC GACCCCACCG 401 AGACGTTCAATCCCGCCGAG TATGAGGCGC AGCTCAACTA CCTGCGCAAC 451 ACCCCGCAGG TGCGCGACGTGCTGCTTTCC GGCGGCGACC CGCTCACACT 501 CGCGCCGAAG GTGCTGGGGC GCCTGCTTTCCGAACTTCGT AAAATCGAGC 551 ACATCGAAAT CATCCGCATC GGCACCCGCG TGCCCGTGTTCATGCCCATG 601 CGCGTGACCC AGGAACTGTG CGACACGCTC GCCGAACACC ATCCGCTGTG651 GATGAACATT CACGTCAACC ACCCCAAGGA AATCACCCCC GAAGTGGCCG 701AGGCGTGTGA CCGTCTGACC CGCGCGGGCG TGCCGCTCGG CAACCAGAGC 751 GTGCTGCTGCGCGGCGTGAA CGACCACCCG GTCATCATGC AAAAGCTGCT 801 GCGCGAGCTC GTCAAAATTCGGGTGCGCCC CTACTACATC TACCAGTGCG 851 ACCTCGTGCA CGGCGCTGGG CACCTGCGCACCACGGTCAG TAAGGGTCTG 901 GAAATCATGG AATCGCTGCG CGGCCACACC TCCGGCTACAGCGTGCCGAC 951 CTACGTGGTG GACGCGCCCG GCGGCGGCGG CAAGATTCCG GTGGCGCCCA1001 ACTACGTGCT CTCGCACAGC CCTGAGAAGC TGATTCTGCG CAACTTCGAG 1051GGCTACATCG CCGCCTACTC GGAGCCCACC GATTACACCG GCCCCGACAT 1101 GGCGATTCCTGACGACTGGA TTCGCAAGGA ACCCGGCCAG ACCGGCATCT 1151 TCGGCCTGAT GGAAGGCGAGCGCATTTCCA TCGAGCCG 1 WQGVPDEQWY DWKWQLKNRI NSVEELQEVL TLTESEYRGASAEGIFRLDI 51 TPYFASLMDP EDPTCPVRRQ VIPTEEELQP FTSMMEDSLA EDKHSPVPGL 101VHRYPDRVLM LVTTQCASYC RYCTRSRIVG DPTETFNPAE YEAQLNYLRN 151 TPQVRDVLLSGGDPLTLAPK VLGRLLSELR KIEHIEIIRI GTRVPVFMPM 201 RVTQELCDTL AEHHPLWMNIHVNHPKEITP EVAEACDRLT RAGVPLGNQS 251 VLLRGVNDHP VIMQKLLREL VKIRVRPYYIYQCDLVHGAG HLRTTVSKGL 301 EIMESLRGHT SGYSVPTYVV DAPGGGGKIP VAPNYVLSHSPEKLILRNFE 351 GYIAAYSEPT DYTGPDMAIP DDWIRKEPGQ TGIFGLMEGE RISIEP

The nucleotide and amino acid sequences (SEQ ID NOs: 13 and 14) of theA. aeolicus polypeptide are:

1 ATGCGTCGCT TTTTTGAGAA TGTACCGGAA AACCTCTGGA GGAGCTACGA 51 GTGGCAGATACAAAACAGGA TAAAAACTCT TAAGGAGATA AAAAAGTACT 101 TAAAACTCCT TCCCGAGGAGGAAGAAGGAA TTAAAAGAAC TCAAGGGCTT 151 TATCCCTTTG CGATAACACC TTACTACCTCTCTTTAATAA ATCCAGAGGA 201 CCCGAAGGAT CCTATAAGAC TTCAGGCAAT CCCCCGCGTTGTAGAAGTTG 251 ATGAAAAGGT TCAGTCTGGG GGAGAACCAG ACGCTCTGAA AGAAGAAGGA301 GATATTCCGG GTCTTACACA CAGGTATCCC GACAGGGTTC TTTTAAACGT 351CACTACCTTT TGTGCGGTTT ACTGCAGGCA CTGTATGAGA AAGAGGATAT 401 TCTCTCAGGGTGAGAGGGCA AGGACTAAAG AGGAAATAGA CACGATGATT 451 GATTACATAA AGAGACAGGAAGAGATAAGG GATGTCTTAA TTTCAGGTGG 501 TGAGCCACTT TCCCTTTCCT TGGAAAAACTTGAATACTTA CTCTCAAGGT 551 TAAGGGAAAT AAAACACGTG GAAATTATAC GCTTTGGGACGAGGCTTCCC 601 GTTCTTGCAC CCCAGAGGTT CTTTAACGAT AAACTTCTGG ACATACTGGA651 AAAATACTCC CCCATATGGA TAAACACTCA CTTCAACCAT CCGAATGAGA 701TAACCGAGTA CGCGGAAGAA GCGGTGGACA GGCTCCTGAG AAGGGGCATT 751 CCCGTGAACAACCAGACAGT CCTACTTAAA GGCGTAAACG ACGACCCTGA 801 AGTTATGCTA AAACTCTTTAGAAAACTTTT AAGGATAAAG GTAAAGCCCC 851 AGTACCTCTT TCACTGCGAC CCGATAAAGGGAGCGGTTCA CTTTAGGACT 901 ACGATAGACA AAGGACTTGA AATAATGAGA TATTTGAGGGGAAGGCTGAG 951 CGGTTTCGGG ATACCCACTT ACGCGGTGGA CCTCCCGGGA GGGAAAGGTA1001 AGGTTCCTCT TCTTCCCAAC TACGTAAAGA AAAGGAAAGG TAATAAGTTC 1051TGGTTTGAAA GTTTCACGGG TGAGGTCGTA GAATACGAAG TAACGGAAGT 1101 ATGGGAACCTTGA 1 MRRFFENVPE NLWRSYEWQI QNRIKTLKEI KKYLKLLPEE EEGIKRTQGL 51YPFAITPYYL SLINPEDPKD PIRLQAIPRV VEVDEKVQSA GEPDALKEEG 101 DIPGLTHRYPDRVLLNVTTF CAVYCRHCMR KRIFSQGERA RTKEEIDTMI 151 DYIKRHEEIR DVLISGGEPLSLSLEKLEYL LSRLREIKHV EIIRFGTRLP 201 VLAPQRFFND KLLDILEKYS PIWINTHFNHPNEITEYAEE AVDRLLRRGI 251 PVNNQTVLLK GVNDDPEVML KLFRKLLRIK VKPQYLFHCDPIKGAVHFRT 301 TIDKGLEIMR YLRGRLSGFG IPTYAVDLPG GKGKVPLLPN YVKKRKGNKF351 WFESFTGEVV EYEVTEVWEP

The nucleotide and amino acid sequences (SEQ ID NOs: 15 and 16) of theT. pallidum polypeptide are:

1 GTGTCTATGG CTGAGTGTAC CCGGGAACAG AGAAAGAGAC GAGGTGCAGG 51 GCGTGCTGATGAGCATTGGC GGACGTTGAG TCCTGCCTCT TGCGCGGCAG 101 ATGCGCTGAC GGAGCATATTTCTCCAGCGT ATGCGCATTT AATTGCACAA 151 GCGCAGGGCG CGGACGCGCA GGCGCTGAAACGTCAGGTGT GCTTTGCGCC 201 ACAGGAGCGT GTGGTGCATG CTTGCGAGTG TGCCGACCCATTGGGTGAGG 251 ACCGGTACTG CGTGACACCC TTTTTGGTGC ATCAGTATGC GAATCGTGTG301 TTGATGTTGG CAACAGGACG TTGCTTTTCA CACTGTCGCT ATTGTTTTCG 351CCGCGGTTTC ATCGCCCAAC GTGCAGGGTG GATCCCCAAC GAAGAGCGCG 401 AGAAGATTATTACGTATCTT CGTGCTACCC CTTCGGTGAA GGAAATCCTG 451 GTTTCAGGTG GTGATCCACTCACTGGTTCT TTTGCACAGG TCACATCGCT 501 TTTCCGCGCA CTGCGCAGTG TAGCGCCGGATTTGATTATT CGTCTGTGCA 551 CTCGCGCAGT CACCTTTGCT CCGCAGGCCT TTACTCCCGAGCTGATTGCG 601 TTTCTGCAGG AGATGAAGCC GGTGTGGATA ATTCCGCATA TTAATCACCC651 GGCAGAGCTC GGTTCTACGC AGCGCGCGGT GCTCGAGGCC TGCGTAGGCG 701CAGGCCTCCC TGTGCAATCG CAGTCGGTAC TGTTGCGCGG GGTGAACGAT 751 TCGGTAGAGACGCTGTGCAC ACTGTTTCAC GCGCTCACTT GTCTGGGGGT 801 TAAGCCGGGG TATCTATTTCAGTTGGATTT GGCGCCTGGA ACTGGGGATT 851 TTCGTGTGCC ACTTTCTGAC ACGCTAGCTCTGTGGCGCAC ATTGAAGGAG 901 CGCCTCTCAG GGTTGTCGCT TCCCACGCTT GCGGTGGACTTGCCAGGGGG 951 TGGAGGAAAG TTTCCGCTTG TGGCATTGGC CTTGCAGCAA GATGTCACGT1001 GGCATCAGGA ACGCGAGGCG TTCTCCGCAC GCGGCATCGA TGGCGCGTGG 1051TACACGTACC CGTTC 1 VSMAECTREQ RKRRGAGRAD EHWRTLSPAS CAADALTEHISPAYAHLIAQ 51 AQGADAQALK RQVCFAPQER VVHACECADP LGEDRYCVTP FLVHQYANRV 101LMLATGRCFS HCRYCFRRGF IAQRAGWIPN EEREKIITYL RATPSVKEIL 151 VSGGDPLTGSFAQVTSLFRA LRSVAPDLII RLCTRAVTFA PQAFTPELIA 201 FLQEMKPVWI IPHINHPAELGSTQRAVLEA CVGAGLPVQS QSVLLRGVND 251 SVETLCTLFH ALTCLGVKPG YLFQLDLAPGTGDFRVPLSD TLALWRTLKE 301 RLSGLSLPTL AVDLPGGGGK FPLVALALQQ DVTWHQEREAFSARGIDGAW 351 YTYPF

Thus, the present invention contemplates the use of clostridial enzymesequences to identify lysine 2,3-aminomutase from other species. Thepresent invention further contemplates variants of such lysine2,3-aminomutases, and the use of such enzymes to prepare β-lysine.

In one screening approach, polynucleotide molecules having nucleotidesequences disclosed herein can be used to screen genomic or cDNAlibraries. Screening can be performed with clostridial lysine2,3-aminomutase polynucleotides that are either DNA or RNA molecules,using standard techniques. See, for example, Ausubel et al. (eds.),SHORT PROTOCOLS IN MOLECULAR BIOLOGY, pages 6-1 to 6-11 (John Wiley &Sons, Inc. 1995). Genomic and cDNA libraries can be prepared usingwell-known methods. See, for example, Ausubel et al. (eds.), SHORTPROTOCOLS IN MOLECULAR BIOLOGY, pages 5-1 to 5-6 (John Wiley & Sons,Inc. 1995).

Additional lysine 2,3-aminomutase genes can also be obtained using thepolymerase chain reaction (PCR) with oligonucleotide primers havingnucleotide sequences that are based upon the nucleotide sequences of thelysine 2,3-aminomutase genes of Clostridium, Porphyromonas, Bacillus,Deinococcus, Aquifex, Teponema, Haemophilus or Escherichia, as describedherein. General methods for screening libraries with PCR are providedby, for example, Yu et al., “Use of the Polymerase Chain Reaction toScreen Phage Libraries,” in METHODS IN MOLECULAR BIOLOGY, Vol. 15: PCRPROTOCOLS: CURRENT METHODS AND APPLICATIONS, White (ed.), pages 211-215(Humana Press, Inc. 1993). Moreover, techniques for using PCR to isolaterelated genes are described by, for example, Preston, “Use of DegenerateOligonucleotide Primers and the Polymerase Chain Reaction to Clone GeneFamily Members,” in METHODS IN MOLECULAR BIOLOGY, Vol. 15: PCRPROTOCOLS: CURRENT METHODS AND APPLICATIONS, White (ed.), pages 317-337(Humana Press, Inc. 1993).

In one instance, the gene from Bacillus subtilus (SEQ ID NO:9) wasisolated from chromosomal DNA by PCR generating an oligonucleotideinsert which after the appropriate restriction digestion was cloned intothe NdeI and XhoI site of pET23a(+) expression vector (Novagen, Inc.,Madison, Wis.). This plasmid construct when placed into E. coli BL21(DE3) cells (Novagen, Inc., Madison, Wis.) and expressed by inductionwith 1 mM isopropyl-beta-thiogalactopyranoside (IPTG) produced cellextracts exhibiting lysine 2,3-aminomutase activity. Cell extracts fromcontrol BL21 (DE3) cells which contained the pET23a(+) vector withoutthe B. subtilus gene and cultured as above demonstrated no measurablelysine 2,3-aminomutase activity.

Anti-lysine 2,3-aminomutase antibodies can also be used to isolate DNAsequences that encode enzymes from cDNA libraries. For example, theantibodies can be used to screen λgt11 expression libraries, or theantibodies can be used for immunoscreening following hybrid selectionand translation. See, for example, Ausubel et al. (eds.), SHORTPROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 6-12 to 6-16 (JohnWiley & Sons, Inc. 1995); and Margolis et al., “Screening λ expressionlibraries with antibody and protein probes,” in DNA CLONING 2:EXPRESSION SYSTEMS, 2nd Edition, Glover et al (eds.), pages 1-14 (OxfordUniversity Press 1995).

6. The Use of Lysine 2,3-Aminomutase to Produce L-β-Lysine

(a) Production of L-β-Lysine Using Purified Enzyme

Recombinant lysine 2,3-aminomutase can be purified from host cells asdescribed above, and used to prepare enantiomerically pure L-β-lysine.An “enantiomerically pure” L-β-lysine comprises at least 87% L-β-lysine.Enantiomerically pure L-β-lysine can be prepared in batchwise reactorsusing soluble lysine 2,3-aminomutase. The lysine 2,3-aminomutase canthen be mixed with the required cofactors: (1) ferrous sulfate or ferricammonium sulfate; (2) pyridoxal phosphate; (3) dehydrolipoic acid,glutathione, or dithiothreitol; (4) S-adenosylmethionine; and (5) sodiumdithionite, and L-lysine at pH 8 or other appropriate pH at atemperature between 25° C. to 37° C., until the production of L-lysineis at equilibrium.

Alternatively, enatiomerically pure L-β-lysine can be obtained bycontinuous processing using immobilized lysine 2,3-aminomutase. Lysine2,3-aminomutase can be packed in a column and activated by the additionof cofactors and a solution containing L-lysine at pH 8 or otherappropriate pH can be passed through the column at a rate that allowscompletion of the reaction during contact with the enzyme. The effluentfrom the column will contain L-β-lysine.

Both of the above methods will produce an equilibrium mixture ofL-β-lysine and L-lysine in which the predominant species is L-β-lysine.The ratio of L-β-lysine to L-lysine after processing is 7:1 whenperformed at pH 8 at 37° C., producing enantiomerically pure L-β-lysine.Chirpich et al., J. Biol. Chem. 245:1778 (1970). If higher purity ofL-β-lysine is desired, the L-lysine can be separated from the L-β-lysineby any number of means well known in the art, including high performancechromatography procedures, such as ion exchange chromatography at anappropriate pH to take advantage of the differences in acidities of thecarboxylic acid groups and the α- and β-ammonium groups of L-lysine andL-β-lysine, respectively.

(b) Production of L-β-Lysine Using Recombinant Host Cells

In an alternative approach, L-β-lysine is produced by fermentation usingrecombinant host cells that over-express cloned lysine 2,3-aminomutase.General methods for high level production of amino acids from culturedbacteria are well-known to those of skill in the art. See, for example,Daugulis, Curr. Opin. Biotechnol. 5:192 (1994); Lee, TIBTECH14:98(1996).

The gene for lysine 2,3-aminomutase can be incorporated into an E. coliplasmid that carries necessary markers and E. coli regulatory elementsfor overexpression of genes. When codon usage for the lysine2,3-aminomutase gene cloned from Clostridia is inappropriate forexpression in E. coli, the host cells can be cotransformed with vectorsthat encode species of tRNA that are rare in E. coli but are frequentlyused by Clostridia. For example, cotransfection of the gene dnaY,encoding TRNA^(ArgAGA/AGG), a rare species of tRNA in E. coli, can leadto high-level expression of heterologous genes in E. coli. Brinkmann etal., Gene 85:109 (1989) and Kane, Curr. Opin. Biotechnol. 6:494 (1995).Heterologous host cells expressing lysine 2,3-aminomutase can becultured with favorable energy, carbon and nitrogen sources underconditions in which L-lysine in the medium is absorbed by the cells andconverted intracellularly into L-β-lysine by lysine 2,3-aminomutase.Unused L-β-lysine will be excreted into the growth medium. L-β-lysinecan then be purified from the medium by any methods well known in theart, including high performance chromatography procedures previouslydescribed.

The present invention, thus generally described, will be understood morereadily by reference to the following examples, which are provided byway of illustration and are not intended to be limiting of the presentinvention.

EXAMPLE 1 Isolation of Clostridial Lysine 2,3-Aminomutase Gene

Lysine 2,3-aminomutase was purified from Clostridia subterminale SB4cells (American Type Culture Collection, Rockville, Md.) according tothe procedure of Moss and Frey, J. Biol. Chem. 265:18112 (1990), asmodified by Petrovich et al., J. Biol. Chem. 226:7656 (1991). Thepurified protein (200 μM—subunit concentration) was dialyzed overnight(1 vol. protein to 1000 vol. 1 mM NaCl) and lyophilized to dryness undervacuum.

The dried lysine 2,3-aminomutase was resuspended to the original volumein 6M guanidine hydrochloride +0.25 M tris(hydroxymethyl)aminomethane(Tris-HCl) pH 8.5+1 mM ethylenediaminetetraacetic acid (EDTA). Theprotein was then reduced with dithiothreitol (DTT) (5 fold molar excessof DTT over cysteine residues) for 3 hours at 25° C. under argonatmosphere and alkylated with 4-vinylpyridine (Aldrich Chemical Co.,Milwaukee, Wis.) (20 fold molar excess over DTT) for 90 minutes at 25°C. The protein sample was dialyzed against distilled water (1 vol.protein to 1000 vol. water) overnight at 4° C., then lyophilized todryness. The dried protein was dissolved in 0.1 N hydrochloric acid(HCl) and subjected to cyanogen bromide (Aldrich Chemical Co.,Milwaukee, Wis.) cleavage by the addition of 100 fold molar excess ofcyanogen bromide to methionine residues under argon gas for 24 hours at25° C. The sample was dried by Speed-Vac (Savant Instruments, Inc.,Hicksville, N.Y.) under vacuum and redissolved in 6M guanidinehydrochloride.

Cyanogen bromide treatment of proteins produces peptide bond cleavage atthe C-terminus side of methionine residues. In the process, cyanogenbromide reacts with the sulfur atom of the thioether side chain ofmethionine to produce homoserine (Practical Protein Chemistry, Wiley,N.Y., (1986) pp. 83-88). Cyanogen bromide treatment of lysine2,3-aminomutase produced 8 major polypeptides. These polypeptides wereseparated from each other using high pressure liquid chromatography(HPLC) and a Vydac C₄ reverse phase column (Vydac 214TP54, 5 M, 4.6×250mm, The Separations Group, Hesperia, Calif.). The polypeptides werefirst separated into five main groups using a linear gradient of 0-80%acetonitrile in 0.1% trifluoroacetic acid (TFA) in water over 60 minutesat a flow rate of 1 ml/min. at room temperature. The individualfractions were collected, dried by Speed-Vac under vacuum, reinjectedinto the same column and eluted with a narrow linear gradient ofacetonitrile in 0.1% TFA. Five individual gradients were used toseparate 8 polypeptides.

The following linear gradients of acetonitrile in 0.1% trifluoroaceticacid in water at 1 ml/min were used: peptide 1—(5-20% 1 hr.); peptide2—(5-25% 1 hr.); peptide 3a—(30-42% 6 hr.); peptide 3b—(30-42% 6 hr.);peptide 4a—(33-50% 6 hr.); peptide 4b—(33-42% 6 hr.); peptide 4c—(33-42%6 hr.); peptide 5 (45-55% 6 hr.). All peptides except peptide 3 a wererepresented as single peaks on the chromatogram when detected at 210 mn.Peptide 3a represented approximately five unresolved peaks on thechromatogram even when the narrow elution gradient was applied.Subsequent analysis of peptide 3a by electrospray mass spectrometry (UWBiotechnology Department, Madison, Wis.) indicated only one peptidespecies of molecular weight of 6664 Da. Thus the multiple peaks observedby HPLC were the result of chromatographic artifact.

Each polypeptide fraction was analyzed for homoserine by acid (HCl)hydrolysis of the peptide, derivatization of the amino acids produced byreaction with phenylisothiocyanate, and separation and quantification ofindividual amino acids. Samples collected from HPLC were dried bySpeed-Vac. Each peptide was dissolved in 6N HCl, placed in a vacuumhydrolysis tube (1 ml, 8×60 mm, Pierce Chemical, Rockford, Ill.), placedunder vacuum, and incubated at 110° C. for 24 hours. Followinghydrolysis, the samples were dried by Speed-Vac. Derivatization,separation, and quantification of amino acids were conducted accordingto Heinrikson et al., Anal. Biochem. 136:65 (1984). One peptide fractioncontaining a low level of homoserine (peptide 3a) was tentativelyidentified as the C-terminus peptide.

The complete protein and peptide 3 a were each sequenced 12-16 aminoacids downstream from the N-terminus (Michigan State University,Department of Biochemistry, Macromolecular Facility, East Lansing,Mich.). The amino acid sequence information was used to designdegenerate oligonucleotides at the N-terminus region of the wholeprotein and the N-terminus region of peptide 3a which served as primersfor polymerase chain reaction (PCR). The N-terminus amino acid sequenceof the complete protein used for primer design was: (SEQ ID NO: 17)KDVSDA corresponding to the (+) DNA strand (SEQ ID NO: 18)5′-AARGAYGTIWSIGAYGC-3′ where I=INOSINE, S=G+C, W=A+T, Y=C+T, D=G+A+T,R=A+G. The N-terminus amino acid sequence of peptide 3a used for primerdesign was: (SEQ ID NO:19) QSHDKV corresponding to the opposite (−)strand (SEQ ID NO:20) 5′-ATIACYTTRTCRTGISWYTG-3′ where I=INOSINE, Y=C+T,R=A+G, S=G+C, W=A+T.

PCR was subsequently used to generate an oligonucleotide of 1029 baseswhich when cloned and sequenced represented approximately 82 percent ofthe entire gene of 1251 bases for lysine 2,3-aminomutase. PCR wasconducted in the following manner. Chromosomal DNA from Clostridiumsubterminale SB4 was prepared and purified utilizing a commerciallyavailable kit: Qiagen Genomic Tip 500/G #13343 (Qiagen, Inc., SantaClarita, Calif.). After ethanol precipitation, the genomic DNA wasresuspended in TE (pH 8.0) buffer (10 mM Tris-HCl pH 8.0+1 mM EDTA). ThePCR reaction mixture (100 μl total volume) contained: Clostridiumsubterminale SB4 chromosomal DNA—2 μg; low salt PCR buffer (Stratagene,La Jolla, Calif.); dNTPs—0.2 mM; oligonucleotide primers—10 μM each; TaqPlus Long DNA Polymerase (Stratagene) -5 units. All samples wereoverlayered with 100 μl mineral oil and subjected to 35 cycles of 1 min.at 94° C., 30 sec. at 37° C., 15 sec. at 50° C., and 3 min. at 72° C.After thermocycling, DNA formed during the PCR process was purified byagarose electrophoresis (2% agarose, Promega Corp., Madison, Wis.) inTAE buffer (0.04 M Tris-acetate pH 8.0+1 mM EDTA). Followingidentification and excision of appropriately sized (1 kbase) ethidiumbromide stained band, DNA was extracted from the agarose using GeneluteMinus EtBr spin column (Supelco, Bellefonte, Pa.), concentrated byprecipitation with ethanol and resuspended in TE pH 8.0 buffer.

DNA obtained from PCR was cloned directly into the pCR2.1 vector (TACloning Kit #K2000-01, Invitrogen Corp., San Diego, Calif.) according tomanufacturer's procedure. Either 12.8 ng or 38.4 ng of PCR insert wasligated to 50 ng pCR2.1 vector overnight at 14° C. Competent E. colicells (Top10F′ One Shot cells—Invitrogen Corp.) were transformed withligation mix (either 12 or 36 ng DNA per 50 μl of cells) and whitecolonies chosen after cells were plated on Luria broth (LB) 10 cm plates(10 gm Difco Bactotryptone, 5 gm Difco Bacto yeast extract, 10 gm NaCl,15 gm Bactoagar per liter water; Difco Laboratories, Detroit, Mich.)containing carbenicillin (100 μg/ml) (Sigma Chemical Co., St. Louis,Mo.) and overlayered with 40 μl isopropyl-α-thiogalactopyranoside (IPTG)(100 mM) (Promega Corp., Madison, Wis.) and 40 μl5-bromo-4-chloro-3-indoyl-β-D-galactoside (X-Gal) (40 mg/ml) (PromegaCorp.). Selected colonies were cultured in LB (10 gm DifcoBactotryptone, 5 gm Difco Bacto yeast extract, 10 gm NaCl per literwater; Difco Laboratories) with carbenicillin (100 μg/ml) for plasmidDNA purification. Plasmid DNA was isolated by either the Qiagen Plasmidmini or midi kits (Qiagen, Inc.).

The PCR insert was sequenced in both strands beginning at the ligationsites by the radiolabeled dideoxynucleotide Sanger method (Sanger, F. etal., Proc. Natl. Acad. Sci. USA 74:5463 (1977) using T7 Sequenaseversion 2.0 Sequencing Kit (Amersham Life Science, Arlington Heights,Ill.). The procedure produced a sequence of 1029 base pairs whichrepresented 82 percent of the entire gene. The remaining unknownsequence of the gene was obtained by preparing a genomic library ofClostridium subterminale SB4 chromosomal DNA. Prior to the preparationof the genomic library, additional information was obtained regardingthe composition of the peptides obtained from cyanogen bromide treatmentof the reduced and alkylated lysine 2,3-aminomutase protein. Themolecular weight of the intact protein and the individual peptides (bothalkylated) were obtained by electrospray mass spectrometry (UWBiotechnology Dept, Madison, Wis.). The molecular weights obtained were:peptide 1—2352; peptide 2—1875; peptide 3a—6664; peptide 3b—6229;peptide 4a—7768; peptide 4b—7403; peptide 4c—6972; peptide 5—8003.Summation of these molecular weights plus the molecular weights of twosmall peptides not observed by HPLC but seen from the translated basesequence (MW=216 and 415) and the N-terminus methionine (MW=149) plusthe additional mass of replacement of 9 homoserines with 9 methionines(ΔMW=270) and minus ten water molecules (ΔMW=180) gives a calculatedmolecular weight of 48,136. Within experimental error, the summation ofthe molecular weights of individual peptides compares with the molecularweight of the reduced and alkylated lysine 2,3-aminomutase protein of48,281 obtained by electrospray mass spectrometry.

Comparison of the molecular weights of the peptides from massspectrometry with the molecular weights of the peptides produced bytranslation of the known incomplete base sequence (1029 base pairs) ofthe protein identified all but two of the peptides. These peptides werepeptide 3a and peptide 2. Since the N-terminus sequence of peptide 3ahad been used for PCR to produce the sequence of 1029 base pairs and allother peptides except peptide 2 had been identified in this knownsequence, peptide 2 must be the C-terminus peptide. Both peptides 2 and3a were subjected to extensive N-terminus amino acid sequence analysis(Michigan State University, Department of Biochemistry, MacromolecularFacility, East Lansing, Mich.). Furthermore, C-terminus amino acidsequence analysis was conducted on the whole protein. For peptide 3a,the N-terminal amino acid sequence reported was: (SEQ ID NO:21)PNYVISQSHDKVILRNFEGVITTYSEPINYTPGCNCDVCTGKKKVHKV. For peptide 2, theN-terminal amino acid sequence reported was: (SEQ ID NO:22)ALEPVGLERNKRHVQ. For the whole protein, the N-terminus amino acidsequence reported was: (SEQ ID NO:23) MINRRYELFKDVSDAD and theC-terminus amino acid sequence reported was: EQV.

A nondegenerate, nonradioactive probe (500 bases) containing digoxygenindUMP residues randomly incorporated was prepared by PCR (The PCR DIGPROBE Synthesis kit -#1636-090 Boehringer-Mannheim, Indianapolis, Ind.).The digoxygenin dUMP groups replace thymidine in some of the positionsof the DNA. The following primers were used for the PCR Probe Synthesiskit: Primer 1 (+) strand (SEQ ID NO:24) -5 ′-ATCCTAACGATCCTAATGATCC;Primer 2 (−) strand (SEQ ID NO:25) -5′-TGGATGGTTAAAGTGAGTG. Using astemplate a plasmid containing the incomplete lysine 2,3-aminomutasegene, the following probe labeled with digoxygenin groups was prepared:(SEQ ID NO:26)5′-ATCCTAACGATCCTAATGATCCAGTAAGAAAACAAGCTATTCCAACAGCATTAGAGCTTAACAAAGCTGCTGCAGATCTTGAAGACCCATTACATGAAGATACAGATTCACCAGTACCTGGATTAACTCACAGATATCCAGATAGAGTATTATTATTAATAACTGATATGTGCTCAATGTACTGCAGACACTGTACAAGAAGAAGATTTGCAGGACAAAGCGATGACTCTATGCCAATGGAAAGAATAGATAAAGCTATAGATTATATCAGAAATACTCCTCAAGTTAGAGACGTATTATTATCAGGTGGAGACGCTCTTTTAGTATCTGATGAAACATTAGAATACATCATAGCTAAATTAAGAGAAATACCACACGTTGAAATAGTAAGAATAGGTTCAAGAACTCCAGTTGTTCTTCCACAAAGAATAACTCCAGAACTTGTAAATATGCTTAAAAAATATCATCCAGTATGGTTAAACACTCACTTTAACCATCCA-3′. Primers (1 μM) were used with plasmid template (1 ng)for PCR according to manufacturer's specifications (Boehringer-Mannheim,Indianapolis, Ind.). The PCR product, checked by agarose gelelectrophoresis, was used directly in probe analysis.

Clostridium subterminale SB4 chromosomal DNA was isolated as describedpreviously and subjected to restriction digestion using severalrestriction endonucleases. These enzymes did not cut in the region ofthe known lysine 2,3-aminomutase gene sequence. However, these siteswere present in the multicloning region of pUC19 vector. The enzymesused were EcoRI (New England Biolabs, Beverly, Mass.), XbaI (PromegaCorp., Madison, Wis.), AccI (New England Biolabs, Beverly, Mass.), andNdeI (Promega Corp., Madison, Wis.). Restriction enzyme (100 units) wasreacted with chromosomal DNA (10 μg) and appropriate buffer(manufacturers specification)+0.01% bovine serum albumin for 90 min. at37° C. in eight replicates. After restriction digestion, each fractionwas applied to a preparative agarose gel (14×14 cm) in multiple lanes inTAE buffer (0.04 M Tris-acetate pH 8.0+1 mM EDTA) and subjected toelectrophoresis at 150 volts. After electrophoresis, several lanes wereseparated from the remaining gel for probe analysis, treated with NaOH(0.5 N) solution to denature DNA, neutralized with 0.5 M Tris-HCl bufferpH 7.5, in preparation for blotting by diffusion. To the surface of thisgel, nylon membrane (#1209-299 Boehringer-Mannheim, Indianapolis, Ind.)was applied followed by filter paper and a stack of paper towel. After24 hr., the paper towel was removed and the nylon membrane treated fordigoxygenin dUMP labeled probe analysis according to manufacturer'sprocedure (Boehringer Mannheim, Indianapolis, Ind.). Positiveprobe-template interaction was identified by chemiluminescence from ananti-digoxygenin antibody conjugate containing alkaline phosphatase andreacting with CDP-Star (disodium 2-chloro-5-(4-methoxyspiro{1,2-dioxetane-3,2′-(5′-chloro) tricyclo [3.3.1.1.]decan}-4-yl)-1-phenylphosphate), a chemiluminescent substrate (both obtained fromBoehringer-Mannheim, Indianapolis, Ind.). The restriction digestionproduced fragments of chromosomal DNA showing positive chemiluminescentprobe-template interaction of the following sizes: XbaI—4.3 kb,EcoRI—4.5 kb, AccI—5.9 kb, and NdeI—6.1 kb. From this information, theappropriate sized fragments of DNA were cut out of zones of theremaining agarose gel. DNA was extracted from these agarose bands by useof spin columns (GenElute Agarose spin column #5-6500, Supelco,Bellefonte, Pa.) by centrifugation at 12,000×g for 10 min. andconcentrated by ethanol precipitation.

Chromosomal DNA fragments were ligated to pUC19 plasmid vector (NewEngland Biolabs, Beverly, MA) cut with the same restriction endonucleaseand dephosphorylated, transformed into competent E. coli XL-2 BlueUltracompetent cells (#200151, Stratagene, La Jolla, Calif.), and platedon LB agar+carbenicillin+X-Gal+IPTG (as previously described). PUC19plasmid vector (10 μg) was incubated with respective restriction enzymes(2 units) in appropriate buffer (manufacturer's specification)+0.01%bovine serum albumin for 1 hour at 37° C. Restriction enzyme activitywas removed from the medium either by passage through a Micropure EZEnzyme Spin column (Amicon, Inc., Beverly, Mass.) or by heatinactivation at 65° C. for 20 min. Each restriction digested pUC19plasmid was dephosphorylated by treatment with 1 unit of calf intestinealkaline phosphatase (Pharmacia Biotech., Piscataway, N.J.) inappropriate buffer (manufacturer's specification) for 30 min. at 37° C.Alkaline phosphatase was removed by using a Micropure EZ Spin column.Plasmid DNA was purified by agarose electrophoresis in TAE buffer (aspreviously described). After ethidium bromide staining, appropriate sizefragments of DNA (approximately 2600 base pairs) were cut out of theagarose. DNA was extracted from the agarose bands with spin columns(GenElute Minus EtBr Spin column, #5-6501, Supelco, Bellefonte, Pa.) bycentrifugation at 14,000×g for 20 min. and concentrated by ethanolprecipitation.

For ligation, 10 ng of restriction endonuclease cut and alkalinephosphatase dephosphorylated vector was ligated to the followingchromosomal DNA inserts to produce a 1:1 or 1:3 ratio of vector DNA toinsert DNA: XbaI—16 and 48 ng, EcoRI—17 and 50 ng, AccI—22 and 66 ng,and NdeI—23 and 68 ng each in a total volume of 10 μl. T4 DNA ligase (3units—Pharmacia Biotech, Piscataway, N.J.) was added to T4 DNA ligasebuffer (Promega Corp., Madison, Wis.) and ligation occurred for 16 hoursat 14° C. Transformed E. coli XL-2 Blue Ultracompetent cells fromindividual plated white colonies (approximately 500 per trial) wereplaced on nylon membranes, treated with alkali to expose and denatureDNA, and hybridized with the oligonucleotide probe labeled withdigoxygenin dUMP (procedures according to manufacturer's specifications,Boehringer-Mannheim, Indianapolis, Ind.). Colonies (1 or 2 per 500) inwhich the digoxygenin labeled probe demonstrated positivechemiluminescence when examined by X-ray film were chosen for furtherscreening by DNA sequencing. The start codon, ATG, was found in one XbaIcolony (X158). The start (ATG) and the stop (TAA) codon were found inone EcoRI colony (E138). Double stranded DNA from these selectedcolonies were sequenced using the automated ABI Prism Dye TerminatorCycle Sequencing procedure by the University of Wisconsin BiotechnologyDepartment, Madison, Wis. to obtain the final sequence of theClostridium subterminale SB4 gene. The DNA sequence was translated intothe amino acid sequence according to the genetic code. Amino acidsequences obtained from N-terminal and C-terminal amino acid analysis ofthe protein and the cyanogen bromide derived peptides were in perfectagreement with the translated DNA sequence. The molecular weight of thetranslated sequence of amino acids (47,025) agreed within experimentalerror with the molecular weight of Clostridial lysine 2,3-aminomutaseprotein obtained by electrospray mass spectrometry (47,173).

EXAMPLE 2 Incorporation of Clostridia subterminale SB4 Lysine2,3-aminomutase Gene Into E. coli

One of the E. coli colonies containing the pUC19 plasmid with thenucleotide sequence encoding the entire Clostridial lysine2,3-aminomutase gene from the genomic library (E138) was used to preparean expression vector. The Clostridial lysine 2,3-aminomutase gene wasinserted into two commercially available plasmid expression vectors. Theplasmid vector, pET-23a(+) (Novagen, Inc., Madison, Wis.) derived frompBR322 contains the T7 promoter as well as the ribosome binding site ofthe phage T7 major capsid protein upstream from the multi-cloning site.The gene for Clostridial lysine 2,3-aminomutase was inserted into themulti-cloning site. This expression system when cloned into a cell linewhich produces an IPTG (isopropyl-β-thiogalactopyranoside)-inducible T7RNA polymerase has been reported to yield very high levels of manyheterologous gene products (Studier et al., Gene Expression Technologyin Methods in Enzymology 185:60 (1991). The plasmid vector, pKK223-3(Amersham Pharmacia Biotech, Piscataway, N.J.) also derived from pBR322contains a strong tac promoter upstream from the multiple cloning siteand a strong rrnB ribosomal terminator downstream. In lac I^(q) E. colicells, the tac promoter is inducible with IPTG, although uninduced cellswill show a low level of expression of the cloned gene. Both plasmidsconfer ampicillin resistance to E. coli cells.

In order to splice the lysine 2,3-aminomutase gene into the abovevectors so that the start codon is correctly spaced from the respectiveribosome binding site of the vector, PCR was used to generate insertswhich after appropriate restriction digestion could be cloned directlyinto the multicloning site of each vector. The following primers or PCRwere used: for pET-23a(+): (SEQ ID NO:27) (+) strand5′-TACACATATGATAAATAGAAGATATG-3′, (SEQ ID NO:28) (−) strand5′-TAGACTCGAGTTATTCTTGAACGTGTCTC-3′; for pKK223-3, (SEQ ID NO:29) (+)strand 5′-TACAGAATTCATGATAAATAGAAGATATG -3′, (SEQ ID NO:30) (−) strand5′-TAGAAAGCTTTTATTCTTGAACGTGTCTC-3′. The DNA template used was the pUC19 plasmid with the nucleotide sequence encoding the entire Clostridiallysine 2,3-aminomutase gene from the genomic library (E138). pUC19plasmid DNA was isolated by the Qiagen Plasmid mini kit (Qiagen, Inc.,Santa Clarita, Calif.). PCR was conducted as described previously. ThePCR reaction mixture (100 μl total volume) contained: pUC19 plasmidDNA—(400 ng); cloned Pfu DNA polymerase reaction buffer (Stratagene, LaJolla, Calif.); dNTPs—0.2 mM each; oligonucleotide primers—1 μM each;cloned Pfu DNA polymerase (Stratagene, La Jolla, Calif.)—5 units. Allsamples were overlayered with 100 μl mineral oil and subjected to 35cycles of 1 min. at 94° C., 30 sec. at 37° C., 15 sec. at 50° C., and 3min. at 72° C. After thermocycling, DNA formed during the PCR processwas further purified by agarose electrophoresis (2% agarose, PromegaCorp., Madison, WI) in TAE buffer (0.04 M Tris-acetate pH 8.0+1 mMEDTA). Following identification and excision of the appropriately sized(˜1.2 kbase) ethidium bromide stained band, DNA was extracted from theagarose using the GenElute Minus EtBr spin column (Supelco, Bellefonte,Pa.), concentrated by precipitation with ethanol, and resuspended in TEpH 8.0 buffer. The purified PCR product was blunt-end ligated topCR-Script Amp cloning vector (#211188 Stratagene, La Jolla, Calif.)using 0.3 pmoles insert to 0.005 pmoles vector according tomanufacturer's specifications. The ligated DNA was used to transformXL1-Blue MRF′ E. coli cells (Stratagene, La Jolla, Calif.) which weresubsequently plated on LB+carbenicillin+IPTG+X-Gal plates (as previouslydescribed) and cultured overnight. White colonies were chosen andsubcloned in LB+carbenicillin (100 μg/ml) media for plasmidpurification.

Plasmid DNA was purified using Qiagen Plasmid mini kit (Qiagen, Inc.,Santa Clarita, Calif.) and subjected to restriction digestion. For thepET-23a(+) insert, 10 μg of plasmid DNA was cut with NdeI (Promega Corp.Madison, Wis.)—50 units and Xho I (Promega Corp.)—50 units in a totalvolume of 100 μl for 1 hr. at 37° C; for pKK223-3 insert, 10 μg ofplasmid DNA was cut with EcoRI (New England Biolabs, Beverly, Mass.)—100units and HindIII (New England Biolabs)—100 units in a total volume of100 μl for 90 min. at 370 C. The insert DNA was separated from theplasmid DNA by agarose gel electrophoresis (2% agarose in TAE buffer),purified and concentrated as previously described. The expressionvectors, pET-23a(+)—10 μg and pKK223-3—10 μg were similarly cut withNdeI-Xho I and EcoRI-HindIII respectively (as previously described).Additionally the restriction cut vectors were dephosphorylated at the 5′end with calf-intestine alkaline phosphatase (Promega Corp, Madison,Wis.)—1 unit for 30 min. at 37° C., purified by agarose gelelectrophoresis and concentrated by ethanol precipitation (as previouslydescribed). The pET-23a(+) insert and the pET-23a(+) cut vector wereligated with T4 DNA ligase (Promega Corp.). To 3 ng of insert were added10 ng of cut vector in T4 DNA ligase buffer (Promega Corp.) +T4 DNAligase (Promega Corp.)—3 units in a total volume of 10 μl and incubatedfor 16 hr. at 14° C. The pKK223-3 insert and the pKK223-3 cut vectorwere ligated as previously described. Competent E. coli cells (Epicuriancoli XL2-Blue MRF′, Stratagene, La Jolla, Calif.) were transformed with2 μl ligation mix and plated on LB+carbenicillin (100 μg/ml) plates.Individual colonies were subcultured in LB+carbenicillin (100 μg/ml)medium and plasmid DNA isolated using the Qiagen Plasmid DNA mini kit.The insert was sequenced in entirety including both regions of the startand stop codon by the automated ABI Prism Dye Terminator CycleSequencing procedure (Perkin-Elmer, Norwalk, Conn.) by the UW BiotechDept (Madison, Wis.) to confirm the correctness of the construct.

For protein expression, the pET-23a(+)-gene insert expression vector wastransformed into competent BL21(DE3) E. coli cells (Novagen, Madison,Wis.). This cell line is a λDE3 lysogen carrying the gene for T7 RNApolymerase under control of IPTG. For transformation, 20 μl of competentcells were treated with 0.1 μg of plasmid DNA. After transformation, 10μl of cells were plated on LB+carbenicillin (100 μg/ml)+plates and grownovernight at 37° C. Individual colonies were subcultured inLB+carbenicillin (100 μg/ml) overnight at 37° C. and ±1 mM IPTG for 3additional hours. For protein expression, the pKK223-3-gene insertexpression vector was used with the Epicurian coli XL2-Blue MRF′(Stratagene, La Jolla, Calif.) without transfer to another cell line orplaced in E. coli JM109 cells. In the latter case, 100 μl of competentJM109 cells (Stratagene, La Jolla, Calif.) were treated with 5 ng ofplasmid DNA and the cells transformed, plated, and subcultured aspreviously described.

Evaluation of the codon usage for the Clostridial lysine 2,3-aminomutasegene indicated that the most frequently used codon for arginine (AGA) isone of the most infrequently used codons in E. coli. There are 29 AGAcodons for 29 total arginines with two regions containing two or threerepeat AGA near the start codon. From the studies of Kane, CurrentOpinion in Biotech. 6:494 (1995) and Brinkmann, et al., Gene 85:109(1989), the expression of heterologous genes containing a high frequencyof rare codons (particularly AGG and AGA) in E. coli is difficult orimpossible due to low cellular concentrations of the respective tRNA.Brinkmann et al. suggest that the presence of rare AGA codon usage canbe relieved by overexpression of the E. coli dnaY gene, which suppliesthis minor arginine tRNA. The sequence of the E. coli dnaY gene waspublished by Garcia et al., Cell 45:453 (1986). The primary products ofthis gene are RNAs of 180 and 190 nucleotides which are processed invivo to form the mature arginine tRNA of 77 nucleotides.

Cotransfection of E. coli BL21 (DE3) cells with both vectors (pET23a(+)vector and pAlter-EX2 vector containing the dnaY gene) was not requiredfor expression of the Clostridial lysine 2,3-aminomutase gene in E.coli. However, lysine 2,3-aminomutase activity of E. coli cellularextracts without pAlter-Ex2/dnaY were approximately 80% less thancellular extracts with this construct. The specific activity of thepurified enzyme isolated from cells without pAlter-Ex2/dnaY wasapproximately half of that of the enzyme isolated from cells containingthe dnaY gene. The yield of purified enzyme from equivalent amounts ofcells was also decreased by 65% when dnaY was absent. Furthermore, cellgrowth in the absence of the vector containing the dna Y gene wassignificantly decreased. The doubling time of cultured E. coli cellscontaining the pET 23a(+) vector during expression of the lysine2,3-aminomutase gene was approximately four times the doubling time ofthe same E. coli cells with the additional pAlter-Ex2 vector containingthe dnaY gene. Therefore, for long-term stability and maximalexpression, E. coli cells containing both expression vectors wereprepared. The dnaY gene was isolated from E. coli chromosomal DNA byPCR. Primers were prepared which produced a 327 bp insert containingBamHI and EcoRI restriction sites necessary for cloning into pAlter-Ex2plasmid vector (Promega Corp.). This vector has a p 15a origin ofreplication which allows it to be maintained with colE1 vectors such aspET-23a(+) and pKK223-3. Also the presence of this vector conferstetracycline resistance to E. coli. The PCR primers used for pAlter-Ex2were: (SEQ ID NO:31) (+)strand—5′-TATAGGATCCGACCGTATAATTCACGCGATTACACC-3′, (SEQ ID NO:32) −)strand—5′-TAGAGAATTCGATTCAGTCAGGCGTCCCATTATC-3′.

Chromosomal DNA from E. coli JM109 cells (Stratagene, La Jolla, Calif.)was prepared and purified utilizing the Qiagen Genomic Tip 500/G #13343(Qiagen, Inc., Santa Clarita, Calif.). After ethanol precipitation, thegenomic DNA was resuspended in TE (pH 8.0) buffer. The PCR reactionmixture (100 μl total volume) contained: E. coli chromosomal DNA—2.5 μg;cloned Pfu DNA polymerase reaction buffer (Stratagene, La Jolla,Calif.); dNTPs—0.2 mM each; oligonucleotide primers—1 μM each; clonedPfu DNA polymerase (Stratagene, La Jolla, Calif.)—5 units. All sampleswere overlayered with 100 μl mineral oil and subjected to 35 cycles of 1min. at 94° C., 30 sec. at 37° C., 15 sec. at 50° C., and 3 min. at 72°C. After thermocycling, DNA formed during the PCR process was furtherpurified by agarose electrophoresis (2% agarose, Promega Corp., Madison,Wis.) in TAE buffer (0.04 M Tris-acetate pH 8.0+1 mM EDTA). Followingidentification and excision of the appropriately sized (˜320 base pairs)ethidium bromide stained band, DNA was extracted from the agarose usingthe GenElute Minus EtBr spin column (Supelco, Bellefonte, Pa.)concentrated by precipitation with ethanol, and resuspended in TE pH 8.0buffer.

The purified PCR product was blunt-end ligated to pCR-Script Amp cloningvector (Stratagene, La Jolla, Calif.) using 0.3 pmoles insert to 0.005pmoles vector according to manufacturer's specifications. The ligatedDNA was used to transform XL1-Blue MRF′ E. coli cells (Stratagene, LaJolla, Calif.) which were subsequently plated onLB+carbenicillin+IPTG+X-Gal plates (as previously described) andcultured overnight. White colonies were chosen and subcloned inLB+carbenicillin (100 μg/ml) media for plasmid purification. Plasmid DNAwas purified using Qiagen Plasmid mini kit (Qiagen, Inc., Santa Clarita,Calif.) and subjected to restriction digestion. For the pAlter-Ex2insert, 1 μg of plasmid DNA was cut with BamHI (Promega Corp., Madison,Wis.)—10 units and EcoRI (Promega Corp.)—10 units in a total volume of100 μl for 1 hr. at 37° C. The insert DNA was separated from the plasmidDNA by agarose gel electrophoresis (3% agarose in TAE buffer) andpurified and concentrated as previously described. The expressionvector, pAlter-Ex2—10 μg was similarly cut with BamHI and EcoRI (aspreviously described). Additionally the restriction cut vector wasdephosphorylated at the 5′ end with calf-intestine alkaline phosphatase(Promega Corp., Madison, Wis.)—10 units for 1 hr. at 37° C., purified byagarose gel electrophoresis and concentrated by ethanol precipitation(as previously described). The dnaY insert and the pAlter-Ex2 cut vectorwere ligated with T4 DNA ligase (Promega Corp.). To 1.68 ng of insertwere added 10 ng of cut vector in T4 DNA ligase buffer (PromegaCorp.)+T4 DNA ligase (Promega Corp.)—3 units in a total volume of 10 μland incubated for 16 hr. at 14° C. Competent BL21(DE3) cells (Novagen,Madison, Wis.) were transformed with 1 μl of ligation mix and plated onLB +tetracycline (12.5 μg/ml). Individual colonies were subcultured inLB+tetracycline (10 μg/ml) medium and plasmid DNA isolated using theQiagen Plasmid DNA mini kit. The insert was sequenced completely by thedideoxy NTP method previously described to confirm the correctness ofthe construct and found to agree with the expected sequence.

BL21 (DE3) cells with the pAlter-Ex2 vector (dnaY gene) werecotransfected with pET-23a(+) (lysine 2,3-aminomutase gene). CompetentBL21(DE3) cells containing the pAlter-Ex2 dnaY gene insert were preparedas follows: E. coli cells were grown overnight in LB+tetracycline (10μg/ml). These cells were used to innoculate a fresh culture ofLB+tetracycline to give a starting absorbance at 600 nm of 0.1. Thecells were cultured at 37° C. with shaking until reaching an absorbanceof 0.6. Forty ml of this culture were transferred to a centrifuge tubeand centrifuged: at 2000×g for 10 min. at 4° C. To the cell pellet wasadded 10 ml of ice cold 0.1 M MgCl₂. The cell pellet was gentlyresuspended and incubated on ice for 20 min. followed by anothercentrifugation at 2000×g for 10 min. at 4° C. To the cell pellet wasadded 2.5 ml of ice cold 0.1 M CaCl₂. The cell pellet was gentlyresuspended and incubated on ice for an additional 40 min.

The above competent BL21 (DE3) cells containing the p-Alter-EX2 vector(dnaY gene) were then cotransformed separately with pET23a(+) plasmidDNA (lysine 2,3-aminomutase gene). To 20 μl of competent cells on icewas added 0.1 μg of pET23a(+) plasmid DNA. The sample was incubated onice for 30 min. followed by a 45 sec. heat shock at 42° C. and coolingon ice for 2 additional min. SOC medium (80 μl) was added and the cellsincubated at 37° C. with shaking at 220 rpm for 1 hr. The cells wereplated on LB+carbenicillin (100 μg/ml)+tetracycline (12.5 μg/ml) andcultured overnight. Individual colonies were subcultured inLB+carbenicillin (100 μg/ml)+tetracycline (10 μg/ml) overnight at 37° C.

EXAMPLE 3 Expression of Clostridia subterminale SB4 Lysine2,3-aminomutase Gene in E. coli

Expression of the cloned gene Clostridial lysine 2,3-aminomutase gene inE. coli was ascertained by sodium dodecyl sulfate (SDS) polyacrylamidegel electrophoresis (PAGE). A 1 ml aliquot of final cell stocks [E. coliBL21(DE3) cells with pET-23a(+) (lysine 2,3-aminomutasegene)±p-Alter-EX2 vector (dnaY gene)] or [E. coli JM109 or Epicuriancoli XL2-Blue MRF′ with pKK223-3 (lysine 2,3-aminomutase gene)]±IPTG wascentrifuged at 14,000×g for 10 min. at 4° C. to remove cell culturemedia. The cell pellet was resuspended in 0.5 ml of 10 mM of4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (Hepes) pH 7.5buffer containing 0.6 mM CaCl₂ and 50 units deoxyribonuclease I(#D-4527, Sigma Chemical, St. Louis, Mo.). Following cell breakage bysonication using the micro-tip of the Sonic Dismembrator (setting 3 forthree 15 sec intervals) (Model #550, Fisher Scientific, Pittsburgh.Pa.), 30 μl of sonicated cells were added to 100 μl of SDS PAGE samplebuffer (0.06 M Tris-HCl pH 6.8 buffer containing 10%(v/v) glycerol, 0.7M β-mercaptoethanol, 0.025 M bromophenol blue). The cell extract washeated at 95° C. for 5 min. prior to loading (5-20 μl/lane) on a minipolyacrylamide gel (Ready Gel #161-1106, Bio-Rad Laboratories, Hercules,Calif.), run at 150 volts (Ready Gel Cell #165-3125, Bio-RadLaboratories, Hercules, Calif.) at constant voltage until the trackingdye was at the bottom of the gel, and stained with Coomassie Blue R-250stain. Control cell extracts were prepared containing E. coli BL21 (DE3)cells with pET-23a(+) without the gene for lysine 2,3-aminomutase.Analysis of the stained SDS PAGE gel revealed one intensely stained bandcorresponding to a molecular weight of 47 kDa migrating between 40 and50 kDa standard proteins (Benchmark Protein Ladder #10747-012, LifeTechnologies, Gaithersburg, Md.) in all samples containing pET 23a(+) orpKK223-3 expression vectors+Clostridial lysine 2,3-aminomutase gene.This band migrated with the same R_(f) as purified Clostridial lysine2,3-aminomutase. Only a weakly stained band was present in control cellextracts with the above expression vectors without the lysine2,3-aminomutase gene.

A requirement for an anaerobic environment when measuring lysine2,3-aminomutase activity (ie., formation of L-β-lysine from L-α-lysine)was previously demonstrated for the Clostridial enzyme [Moss and Frey,J. Biol. Chem. 265:18112 (1990), Petrovich et al., J. Biol. Chem.226:7656 (1991)]. Therefore all subsequent steps including cell culture,cell extract preparation, and enzyme assay were done in the absence ofoxygen. The following procedure demonstrates the formation of L-β-lysinefrom L-α-lysine in vivo in E. coli cells. BL21(DE3) cells containing thepET23a(+) expression vector for the Clostridial lysine 2,3-aminomutasegene with the expression vector for E. coli dna Y gene were culturedanaerobically at 37° C. in 100 ml of M9 medium (0.68 gm Na₂HPO₄, 0.3 gmKH₂PO₄, 0.05 gm NaCl, 0.1 gm NH₄Cl) containing CaCl₂ (0.1 mM), MgSO₄ (1mM), ZnSO₄ (10 μM), Fe(II)SO₄ (50 μM), D-(+)-glucose (0.2% w/v),ampicillin (100 μg/ml)±tetracycline (10 μg/ml) in 150 ml sealed bottlesmade anaerobic by sparging with nitrogen gas and the addition of 1 mMsodium dithionite and 4 mM sodium thioglycolate (Sigma Chemical Co., St.Louis, Mo.). After cells reached a density of approximately 0.5 OD unitsat 600 nm, L-α-lysine (50 mM) was added and the cells cultured anadditional 16 hrs. at 37° C. anaerobically. Cells were harvested bycentrifugation at 6,000×g for 10 min. and resuspended in 0.5 ml ofdistilled water. Following sonication using the micro-tip of the SonicDismembrator (setting 3 for three 15 sec. intervals) (Model #550—FisherScientific, Pittsburgh. Pa.), the lysed cells were centrifuged at14,000×g for 20 min. at room temperature. The supernatant was used tomeasure formation of L-β-lysine from L-α-lysine resulting from theexpression of the Clostridial lysine 2,3-aminomutase gene in E. coli.Control cells which contained pET 23a(+) plasmid without the Clostridiallysine 2,3-aminomutase gene were also cultured and harvested aspreviously described.

The presence of L-β-lysine in E. coli cell extract was detected bytreating the extract with phenylisothiocyanate (Pierce Chemical Co.,Rockford, Ill.) which derivatizes amino acids to their respectivephenylthiocarbamyl derivatives. These compounds are readily separatedand detected by high pressure liquid chromatography (HPLC). Theprocedure is based on the method of Heinrikson and Meredith, Anal.Biochem. 136:65 (1984): 10 μl of cell extract (see above) were treatedwith 100 μl of coupling buffer(acetonitrile:pyridine:triethylamine:water 10:5:2:3 v/v/v) andevaporated to dryness using a Speed-Vac (Savant Instruments, Inc.,Hicksville, N.Y.). The sample was redissolved in 100 μl coupling bufferand 5 ml of phenylisothiocyanate was added and mixed. After 5 min. atroom temperature, the sample was again dried using the Speed-Vac. Thedried sample was redissolved in distilled water (200 μl) and centrifugedat 14,000×g for 10 min. to remove undissolved material. The sample wasinjected into a Waters HPLC (Millipore Corporation, WatersChromatography Division, Milford, Mass.) equipped with a Vydac C₈reverse phase column (Vydac 208TP54, 5 mM, 4.6×250 mm, The SeparationsGroup, Hesperia, Calif.). The derivatized L-α-lysine and L-β-lysine wereseparated using a linear gradient composed of buffer A (0.05 M ammoniumacetate in water) and buffer B (0.1 M ammonium acetate inacetonitrile:methanol:water (46:10:44 v/v/v) at a flow rate of 1 ml/min.at room temperature and monitored at a wavelength of 254 nm. The initialconditions were 30% buffer B for 2 min. followed by a linear gradient to60% buffer B in 24 min. The retention times for phenylthiocarbamoylderivatives of L-α-lysine was 25.7±0.3 min. and for L-β-lysine was22.9±0.4 min. L-β-lysine (up to 35% of total lysine) was observed in allcell extracts of E. coli cells containing the pET 23a(+) plasmid vectorwith the Clostridial lysine 2,3-aminomutase gene and absent in controlcells which were treated identically but did not contain the plasmidwith the Clostridial lysine 2,3-aminomutase gene.

In vitro formation of β-lysine by E. coli cell extracts was alsomeasured utilizing the standard assay procedure (Ballinger et al.,Biochemistry 31:10782 (1992). The conversion of radiolabeled C-14L-α-lysine to radiolabeled C-14 L-β-lysine was observed in the followingmanner:

Aerobically grown E. coli cells (1 ml) containing the pET 23 a(+)plasmid vector with the Clostridial lysine 2,3-aminomutase gene and thep-Alter-EX2 plasmid vector with the E. coli dnaY gene were used to seeda glass fermentor (Virtis Laboratory Fermentor #233395, VirtisCorporation, Gardiner, N.Y.) containing 15 liters of 2xYT media (240 gmDifco Bactotryptone, 150 gm Bacto yeast extract, 2.5 gm sodium chloride,Difco Laboratories, Detroit, Mich.) and supplemented with 50 μMFe(II)SO₄, 50 μM ZnSO₄, 50 μM Na₂S, 4 mM sodium thioglycolate, 100 μg/mlampicillin, and 10 μg/ml tetracycline. The sealed flask was madeanaerobic by gentle bubbling of nitrogen gas for 3 hours prior to cellinoculation. Anaerobicity was monitored by the presence of a smallquantity of methylene blue (10 mg) which remains colorless in theabsence of oxygen. After approximately 14 hours anaerobic culture at 37°C. when the cell density had reached 0.05 OD (optical density) at 600nm, 0.2% (w/v) D-(+) glucose was added. The culture was allowed tocontinue to 0.7 OD at 600 nm when 1 mM isopropyl-β-thiogalactopyranoside(IPTG) (Fisher Scientific, Pittsburgh, Pa.) was added to induce furtherexpression of the Clostridial lysine 2,3-aminomutase gene. After 4hours, the culture was cooled to 24° C. and allowed to continue for anadditional 12 hours before cell harvesting. Cells were harvested byconcentration using tangential flow filtration (Pellicon System,Millipore Corporation, Bedford, Mass.) followed by centrifugation at5,000×g for 20 min. The cell pellets were snap frozen and stored inliquid nitrogen until used.

All subsequent operations were conducted in an anaerobic glove box (CoyLaboratory Products, Inc. Ann Arbor, Mich.). Cells (approximately 1-2gms) were placed in 3 ml of 0.03 M sodium EPPS buffer(N-[2-hydroxyethylpiperazine-N′-[3-propanesulfonic acid]) pH 8containing 0.1 mM L-α-lysine, 10 μM pyridoxal-5-phosphate, and 1 mMdithiothreitol (Sigma Chemical Co., St. Louis, Mo.). The cells werebroken by sonication (Sonic Dismembrator #550, Fisher Scientific,Pittsburgh, Pa.) using the microtip at a setting of 3 for five 20 sec.bursts with cooling on ice. The broken cells were centrifuged at80,000×gav for 30 min.

The supernatant was used to measure L-β-lysine formation according tothe procedure of Ballinger et al. Biochemistry 31:10782 (1992). Theprocedure is based on the observation that radiolabeled L-a-lysine canbe separated from radiolabeled L-β-lysine by paper electrophoresis informic acid solution based on the difference in the pKa of the carboxylgroup of each amino acid. The cell extract was incubated in 0.04 M EPPSpH 8 buffer containing 1 mM ferrous ammonium citrate, 0.5 mM pyridoxal5-phosphate, and 20 mM dihydrolipoic acid for 4 hr. at 37° C. After thereductive incubation, the sample was diluted into 0.18 M EPPS pH 8buffer containing 3 mM sodium dithionite, 18 μM S-adenosylmethionine, 44mM C-14 labeled (#NEC280E-NEN Life Science Products, Boston, Mass.) andunlabeled L-α-lysine and incubated 4 min. at 37° C. The reaction wasstopped by the addition of 0.2 M formic acid. The mixture was spottedonto chromatography paper (Whatman #3001917, Whatman, LTD, Maidstone,England), the amino acids separated by electrophoresis and radioactivitymeasured according to the published procedure. The cell extractexhibited lysine 2,3-aminomutase activity (4-5 units/mg protein). Thespecific activity of purified lysine 2,3-aminomutase from Clostridiumsubterminale SB4 cells has been reported as 30-40 units/mg (Lieder et.al., Biochemistry 37:2578 (1998)). Thus lysine 2,3-aminomutaserepresents approximately 10-15% of total cellular protein in thisexpression system.

The recombinant produced lysine 2,3-aminomutase was purified accordingto the procedure of Moss and Frey, J. Biol. Chem. 265:18112 (1990) asmodified by Petrovich et al., J. Biol. Chem. 226:7656 (1991), aspreviously discussed. The purified recombinant produced lysine2,3-aminomutase had equivalent enzyme activity (34.5±1.6 μmoles lysinemin¹ m⁻¹ protein) to purified naturally produced Clostridial enzyme(Lieder et al., Biochemistry 37:2578 (1998).

All references cited above are hereby incorporated by reference.

Although the foregoing refers to particular preferred embodiments, itwill be understood that the present invention is not so limited. It willoccur to those of ordinary skill in the art that various modificationsmay be made to the disclosed embodiments and that such modifications areintended to be within the scope of the present invention, which isdefined by the following claims.

1. A method of producing L-β-lysine, comprising: (a) culturing aprokaryotic host cell comprising an expression vector that encodeslysine 2,3-aminomutase in the presence of L-lysine, wherein the vectorthat encodes lysine 2,3-aminomutase has a nucleic acid sequence of SEQID NO: 3 and the cultured host cell expresses lysine 2,3-aminomutase,and (b) isolating L-β-lysine from the cultured host cells.
 2. The methodof claim 1 wherein the isolated L-β-lysine is enantiomerically pure. 3.A method of producing L-β-lysine, comprising: (a) immobilizing lysine2,3-aminomutase on a suitable support, wherein the lysine2,3-aminomutase has the amino acid sequence of SEQ ID NO: 4; (b)activating the lysine 2,3-aminomutase with cofactors required for lysine2,3-aminomutase activity; and (c) contacting L-lysine with theimmobilized lysine 2,3-aminomutase to produce L-β-lysine.
 4. The methodof claim 3 wherein the L-lysine is contacted with the immobilized lysine2,3-aminomutase for a sufficient amount of time to produceenantiomerically pure L-β-lysine.
 5. The method of claim 2 furthercomprising separating the L-β-lysine from the L-lysine.
 6. The method ofclaim 5 wherein the separation of the L-β-lysine from the L-lysine isachieved using high performance chromatography.
 7. The method of claim 2wherein the process is a continuous process.
 8. The method of claim 3wherein the cofactors required for lysine 2,3-aminomutase activitycomprise: (i) at least one of ferrous sulfate or ferric ammoniumsulfate; (ii) pyridoxal phosphate; (iii) at least one of dehydrolipoicacid, glutathione or dithiothreitol; (iv) S-adenosylmethionine; and (v)sodium dithionite.
 9. A method of producing L-β-lysine, comprising: (a)culturing a prokaryotic host cell comprising an expression vector thatencodes lysine 2,3-aminomutase in the presence of L-lysine, wherein thecultured host cell expresses lysine 2,3-aminomutase, and (b) isolatingL-β-lysine from the cultured host cells, wherein the lysine2,3-aminomutase has the amino acid sequence of SEQ ID NO:
 4. 10. Amethod of producing L-β-lysine, comprising: (a) incubating L-lysine in asolution containing purified lysine 2,3-aminomutase, wherein the lysine2,3-aminomutase has the amino acid sequence of SEQ ID NO: 4, saidsolution containing all cofactors required for lysine 2,3-aminomutaseactivity; and (b) isolating L-β-lysine from the incubation solution. 11.The method of claim 10, wherein step (b) further comprises isolatingL-β-lysine from L-lysine via chromatography.